1
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Pian H, Wang H, Wang H, Tang F, Li Z. Capillarity-powered and CRISPR/Cas12a-responsive DNA hydrogel distance sensor for highly sensitive visual detection of HPV DNA. Biosens Bioelectron 2024; 264:116657. [PMID: 39137521 DOI: 10.1016/j.bios.2024.116657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Revised: 07/30/2024] [Accepted: 08/08/2024] [Indexed: 08/15/2024]
Abstract
The rapid and specific identification and sensitive detection of human papillomavirus (HPV) infection is critical for preventing cervical cancer, particularly in resource-limited regions. In this work, we hope to propose a capillarity-powered and CRISPR/Cas12a-responsive DNA hydrogel distance sensor for point-of-care (POC) DNA testing. Using the thermal reversibility of DNA hydrogel and capillarity, the novel DNA hydrogel distance sensor can be rapidly and simply constructed by loading an ultra-thin CRISPR/Cas12a-responsive DNA-crosslinked hydrogel film at the end of the capillary tube. The target DNA-specific recombinase polymerase reaction (RPA) amplicons activate the trans-cleavage activity of the Cas12a enzyme, cleaving the crosslinked DNA in hydrogel film, and causing an increase of hydrogel's permeability. As a result, a sample solution containing target DNA travels into the capillary tube at a longer distance compared to the negative samples. Reading the solution traveling distance in capillary tubes, the novel sensor realizes target DNA detection without any special equipment. Benefiting from the exponential target amplification of RPA and multiple turnover response of trans-cleavage of CRISPR/Cas12a, the developed sensor can visually and specifically detect as low as 1 aM HPV 16 DNA within 30 min. These outstanding features, including exceptional sensitivity and specificity, simple and portable design, mild measurement conditions, quick turnaround time, and user-friendly read-out, make the novel distance sensor a promising option for POC diagnostic applications.
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Affiliation(s)
- Hongru Pian
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - Hui Wang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, China.
| | - Honghong Wang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - Fu Tang
- School of Materials Science and Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - Zhengping Li
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, China.
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2
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Gu X, Tang Q, Zhu Y, Sun C, Wu L, Ji H, Wang Q, Wu L, Qin Y. Advancements of CRISPR technology in public health-related analysis. Biosens Bioelectron 2024; 261:116449. [PMID: 38850734 DOI: 10.1016/j.bios.2024.116449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 05/24/2024] [Accepted: 05/27/2024] [Indexed: 06/10/2024]
Abstract
Pathogens and contaminants in food and the environment present significant challenges to human health, necessitating highly sensitive and specific diagnostic methods. Traditional approaches often struggle to meet these requirements. However, the emergence of the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) system has revolutionized nucleic acid diagnostics. The present review provides a comprehensive overview of the biological sensing technology based on the CRISPR/Cas system and its potential applications in public health-related analysis. Additionally, it explores the enzymatic cleavage capabilities mediated by Cas proteins, highlighting the promising prospects of CRISPR technology in addressing bioanalysis challenges. We discuss commonly used CRISPR-Cas proteins and elaborate on their application in detecting foodborne bacteria, viruses, toxins, other chemical pollution, and drug-resistant bacteria. Furthermore, we highlight the advantages of CRISPR-based sensors in the field of public health-related analysis and propose that integrating CRISPR-Cas biosensing technology with other technologies could facilitate the development of more diverse detection platforms, thereby indicating promising prospects in this field.
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Affiliation(s)
- Xijuan Gu
- School of Public Health, Nantong University, Nantong, Jiangsu, 226019, PR China; Xinglin College, Nantong University, Qidong, Jiangsu, 226236, PR China
| | - Qu Tang
- School of Public Health, Nantong University, Nantong, Jiangsu, 226019, PR China
| | - Yidan Zhu
- Medical School, Nantong University, Nantong, Jiangsu, 226001, PR China
| | - Chenling Sun
- School of Public Health, Nantong University, Nantong, Jiangsu, 226019, PR China
| | - Lingwei Wu
- School of Public Health, Nantong University, Nantong, Jiangsu, 226019, PR China
| | - Haiwei Ji
- School of Public Health, Nantong University, Nantong, Jiangsu, 226019, PR China
| | - Qi Wang
- School of Public Health, Nantong University, Nantong, Jiangsu, 226019, PR China.
| | - Li Wu
- Nantong Key Laboratory of Public Health and Medical Analysis, School of Life Sciences, Nantong University, Nantong, Jiangsu, 226019, PR China; School of Public Health, Nantong University, Nantong, Jiangsu, 226019, PR China.
| | - Yuling Qin
- School of Public Health, Nantong University, Nantong, Jiangsu, 226019, PR China.
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3
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Xie Y, Jiang K, Zhang Y, Cao L, Guo X, Shi J, Ding X, Yin K. Enhanced Two-Step LAMP-CRISPR Assay with an Engineered Zst Polymerase for Contamination-Free and Ultrasensitive DNA Detection. Anal Chem 2024. [PMID: 39250834 DOI: 10.1021/acs.analchem.4c03965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/11/2024]
Abstract
Current loop-mediated isothermal amplification (LAMP)-coupled clustered regularly interspaced short palindromic repeats (LAMP-CRISPR) biosensing in two-step or one-step formats has been applied to next-generation accurate molecular diagnosis. However, two-step LAMP-CRISPR assays intrinsically confront aerosol contamination, while one-step assays possess a compromised detection performance. To this end, we propose an enhanced two-step LAMP-CRISPR assay (ETL-CRISPR) with an engineered Zst polymerase to mediate ultrasensitive DNA detection and thoroughly eliminate aerosol contamination. Instead of supplementing any dTTP, the newly engineered Zst polymerase can efficiently polymerize four oligonucleotides (dATP, dCTP, dGTP, and dUTP), thereby enabling contamination-free and ultrasensitive ETL-CRISPR assay. By targeting the L1 gene of human papillomaviruses (HPV) 16 and the E7 gene of HPV18, our ETL-CRISPR assay achieves high specificity and single-copy level sensitivity within 1 h. Furthermore, we validated the assay by using 85 HPV clinical swab samples with an accuracy of 98.8%, which is comparable to the real-time quantitative polymerase chain reaction. Therefore, ETL-CRISPR provides a straightforward strategy for the contamination-free and ultrasensitive point-of-care diagnosis of clinical pathogens.
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Affiliation(s)
- Yi Xie
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, P. R. China
- One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai 200127, P. R. China
| | - Kai Jiang
- Department of Biobank, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, P. R. China
| | - Yuqian Zhang
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota 55905, United States
| | - Liqin Cao
- Hunan Xiansai Institute, Changsha 410000, P. R. China
| | - Xiaokui Guo
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, P. R. China
- One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai 200127, P. R. China
| | - Jun Shi
- Department of Obstetrics and Gynecology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, P. R. China
| | - Xiong Ding
- Key Laboratory of Environmental Medicine and Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, P. R. China
- Department of Nutrition and Food Hygiene, School of Public Health, Southeast University, Nanjing 210009, P. R. China
| | - Kun Yin
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, P. R. China
- One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai 200127, P. R. China
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4
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Zhao C, Du L, Hu J, Hou X. Recombinase Polymerase Amplification and Target-Triggered CRISPR/Cas12a Assay for Sensitive and Selective Hepatitis B Virus DNA Analysis Based on Lanthanide Tagging and Inductively Coupled Plasma Mass Spectrometric Detection. Anal Chem 2024. [PMID: 39241168 DOI: 10.1021/acs.analchem.4c03715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/08/2024]
Abstract
Herein, we report a target-triggered CRISPR/Cas12a assay by coupling lanthanide tagging and inductively coupled plasma mass spectrometry (ICP-MS) for highly sensitive elemental detection. Hepatitis B virus (HBV) DNA was chosen as a model analyte, and recombinase polymerase amplification (RPA) was used for target amplification. The double-stranded RPA amplicons containing a 5' TTTG PAM sequence can be recognized by Cas12a through a specific CRISPR RNA, activating the trans-cleavage activity of CRISPR/Cas12a and nonspecific cleavage of terbium (Tb)-ssDNA modified on magnetic beads (MBs). Following magnetic separation and acid digestion, the released Tb3+ ions were quantitated by ICP-MS and correlated to the concentration of HBV DNA. Taking advantage of the accelerated cleavage of Tb-ssDNA attached to the MB particles, RPA for target amplification, and ICP-MS for highly selective signal readout, this method permits the detection of 1 copy/μL of HBV DNA in serum with high specificity and holds great promise in the early diagnosis of viral infections or tumor development.
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Affiliation(s)
- Chenxi Zhao
- Analytical & Testing Center, Sichuan University, Chengdu, Sichuan 610064, China
| | - Lijie Du
- Analytical & Testing Center, Sichuan University, Chengdu, Sichuan 610064, China
| | - Jing Hu
- Analytical & Testing Center, Sichuan University, Chengdu, Sichuan 610064, China
| | - Xiandeng Hou
- Analytical & Testing Center, Sichuan University, Chengdu, Sichuan 610064, China
- Key Lab of Green Chem & Tech (MOE) at College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
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5
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He W, Li X, Li X, Guo M, Zhang M, Hu R, Li M, Ding S, Yan Y. Exploration of new ways for CRISPR/Cas12a activation: DNA hairpins without PAM and toehold and single strands containing DNA and RNA bases. J Biotechnol 2024; 391:99-105. [PMID: 38880387 DOI: 10.1016/j.jbiotec.2024.06.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 06/07/2024] [Accepted: 06/13/2024] [Indexed: 06/18/2024]
Abstract
The CRISPR/Cas12a system is emerging as a promising candidate for next-generation diagnostic biosensing platforms, with the discovery of new activation modes greatly expanding its applications. Here, we have identified two novel CRISPR/Cas12a system activation modes: PAM- and toehold-free DNA hairpins, and DNA-RNA hybrid strands. Utilizing a well-established real-time fluorescence method, we have demonstrated a strong correlation between DNA hairpin structures and Cas12a activation. Compared with previously reported activation modes involving single-stranded DNA and PAM-contained double-stranded DNA, the DNA hairpin activation way exhibits similar specificity and generality. Moreover, our findings indicate that increasing the number of RNA bases in DNA-RNA hybrid strands can decelerate the kinetics of Cas12a-triggered trans-cleavage of reporter probes. These newly discovered CRISPR/Cas12a activation ways hold significant potential for the development of high-performance biosensing strategies.
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Affiliation(s)
- Wen He
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, PR China
| | - Xinyu Li
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, PR China
| | - Xinmin Li
- Chongqing Key Laboratory of Sichuan-Chongqing Co-construction for Diagnosis and Treatment of Infectious Diseases Integrated Traditional Chinese and Western Medicine, Chongqing Hospital of Traditional Chinese Medicine, Chongqing 400021, PR China
| | - Minghui Guo
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, PR China
| | - Mengxuan Zhang
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, PR China
| | - Ruiwei Hu
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, PR China
| | - Menghan Li
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, PR China
| | - Shijia Ding
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, PR China
| | - Yurong Yan
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, PR China.
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6
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Liu J, Li N, Zhang L, Lu Y, Shen M, Zhang Y, Feng L, Jing J, Cheng J, Xu Y. A Wax Interface-Enabled One-Pot Multiplexed Nucleic Acid Testing Platform for Rapid and Sensitive Detection of Viruses and Variants. SMALL METHODS 2024; 8:e2400030. [PMID: 38716631 DOI: 10.1002/smtd.202400030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 04/16/2024] [Indexed: 08/18/2024]
Abstract
High-quality, low-cost, and rapid detection is essential for the society to reopen the economy during the critical period of transition from Coronavirus Disease 2019 (COVID-19) pandemic response to pandemic control. In addition to performing sustainable and target-driven tracking of SARS-CoV-2, conducting comprehensive surveillance of variants and multiple respiratory pathogens is also critical due to the frequency of reinfections, mutation immune escape, and the growing prevalence of the cocirculation of multiple viruses. By utilizing a 0.05 cents wax interface, a Stable Interface assisted Multiplex Pathogenesis Locating Estimation in Onepot (SIMPLEone) using nested RPA and CRISPR/Cas12a enzymatic reporting system is successfully developed. This smartphone-based SIMPLEone system achieves highly sensitive one-pot detection of SARS-CoV-2 and its variants, or multiple respiratory viruses, in 40 min. A total of 89 clinical samples, 14 environmental samples, and 20 cat swab samples are analyzed by SIMPLEone, demonstrating its excellent sensitivity (3-6 copies/reaction for non-extraction detection of swab and 100-150 copies/mL for RNA extraction-based assay), accuracy (>97.7%), and specificity (100%). Furthermore, a high percentage (44.2%) of co-infection cases are detected in SARS-CoV-2-infected patients using SIMPLEone's multiplex detection capability.
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Affiliation(s)
- Jiajia Liu
- School of Biomedical Engineering, Tsinghua University, Beijing, 100084, China
- CapitalBiotech Technology, Beijing, 101111, China
| | - Nan Li
- State Key Laboratory of Transducer Technology, Aerospace Information Research Institute of Chinese Academy of Sciences, Beijing, 100190, China
| | - Li Zhang
- School of Biomedical Engineering, Tsinghua University, Beijing, 100084, China
| | - Ying Lu
- School of Biomedical Engineering, Tsinghua University, Beijing, 100084, China
| | - Minjie Shen
- School of Biomedical Engineering, Tsinghua University, Beijing, 100084, China
| | - Yuanyue Zhang
- School of Biomedical Engineering, Tsinghua University, Beijing, 100084, China
| | - Li Feng
- CapitalBiotech Technology, Beijing, 101111, China
| | - Juhui Jing
- CapitalBiotech Technology, Beijing, 101111, China
| | - Jing Cheng
- School of Biomedical Engineering, Tsinghua University, Beijing, 100084, China
- National Engineering Research Center for Beijing Biochip Technology, Beijing, 102200, China
| | - Youchun Xu
- School of Biomedical Engineering, Tsinghua University, Beijing, 100084, China
- CapitalBiotech Technology, Beijing, 101111, China
- National Engineering Research Center for Beijing Biochip Technology, Beijing, 102200, China
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7
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Chen L, Hu M, Zhou X. Trends in developing one-pot CRISPR diagnostics strategies. Trends Biotechnol 2024:S0167-7799(24)00185-9. [PMID: 39095257 DOI: 10.1016/j.tibtech.2024.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Revised: 07/09/2024] [Accepted: 07/12/2024] [Indexed: 08/04/2024]
Abstract
The integration of nucleic acid amplification (NAA) with the CRISPR detection system has led to significant advancements and opportunities for development in molecular diagnostics. Nevertheless, the incompatibility between CRISPR cleavage and NAA has significantly impeded the commercialization of this technology. Currently, several one-pot detection strategies based on CRISPR systems have been devised to address concerns regarding aerosol contamination risk and operational complexity associated with step-by-step detection as well as the sensitivity limitation of conventional one-pot methods. In this review, we provide a comprehensive introduction and outlook of the various solutions of the one-pot CRISPR assay for practitioners who are committed to developing better CRISPR nucleic acid detection technologies to promote the progress of molecular diagnostics.
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Affiliation(s)
- Lin Chen
- School of Life sciences, South China Normal University, Guangzhou 510631, P. R. China
| | - Menglu Hu
- School of Life sciences, South China Normal University, Guangzhou 510631, P. R. China.
| | - Xiaoming Zhou
- School of Life sciences, South China Normal University, Guangzhou 510631, P. R. China; MOE Key laboratory of Laser Life Science & Guangdong Provincial Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, China.
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8
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Wang H, Wang H, Pian H, Su F, Tang F, Chen D, Chen J, Wen Y, Le XC, Li Z. CRISPR/Cas13a-Responsive and RNA-Bridged DNA Hydrogel Capillary Sensor for Point-of-Care Detection of RNA. Anal Chem 2024; 96:12022-12029. [PMID: 39001804 PMCID: PMC11270516 DOI: 10.1021/acs.analchem.4c02087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Revised: 06/07/2024] [Accepted: 06/26/2024] [Indexed: 07/15/2024]
Abstract
Disease diagnostics and surveillance increasingly highlight the importance of portable, cost-effective, and sensitive point-of-care (POC) detection of nucleic acids. Here, we report a CRISPR/Cas13a-responsive and RNA-bridged DNA hydrogel capillary sensor for the direct and visual detection of specific RNA with high sensitivity. The capillary sensor was simply prepared by loading RNA-cross-linking DNA hydrogel film (∼0.2 mm ± 0.02 mm) at the end of a capillary. When CRISPR/Cas13a specifically recognizes the target RNA, the RNA bridge in the hydrogel film is cleaved by the trans-cleavage activity of CRISPR/Cas13a, increasing the permeability of the hydrogel film. Different concentrations of target RNA activate different amounts of Cas13a, cleaving different amounts of the RNA bridge in the hydrogel and causing corresponding changes in the permeability of the hydrogel. Therefore, samples containing different amounts of the target RNA travel to different distances in the capillary. Visual reading of the distance provides quantitative detection of the RNA target without the need for any nucleic acid amplification or auxiliary equipment. The technique was successfully used for the determination of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in clinical nasopharyngeal (NP) swab and saliva samples. Easily quantifiable distance using a ruler eliminates the need for any optical or electrochemical detection equipment, making this assay potentially useful for POC and on-site applications.
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Affiliation(s)
- Hui Wang
- Beijing
Key Laboratory for Bioengineering and Sensing Technology; School of
Chemistry and Biological Engineering, University
of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China
- Division
of Analytical and Environmental Toxicology, Department of Laboratory
Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
| | - Honghong Wang
- Beijing
Key Laboratory for Bioengineering and Sensing Technology; School of
Chemistry and Biological Engineering, University
of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China
- Division
of Analytical and Environmental Toxicology, Department of Laboratory
Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
| | - Hongru Pian
- Beijing
Key Laboratory for Bioengineering and Sensing Technology; School of
Chemistry and Biological Engineering, University
of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Fengxia Su
- Beijing
Key Laboratory for Bioengineering and Sensing Technology; School of
Chemistry and Biological Engineering, University
of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Fu Tang
- School
of Materials Science and Engineering, University
of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Desheng Chen
- Beijing
Key Laboratory for Bioengineering and Sensing Technology; School of
Chemistry and Biological Engineering, University
of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Junjie Chen
- Beijing
Key Laboratory for Bioengineering and Sensing Technology; School of
Chemistry and Biological Engineering, University
of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Yongqiang Wen
- Beijing
Key Laboratory for Bioengineering and Sensing Technology; School of
Chemistry and Biological Engineering, University
of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China
| | - X. Chris Le
- Division
of Analytical and Environmental Toxicology, Department of Laboratory
Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
| | - Zhengping Li
- Beijing
Key Laboratory for Bioengineering and Sensing Technology; School of
Chemistry and Biological Engineering, University
of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China
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9
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Ye X, Wu H, Liu J, Xiang J, Feng Y, Liu Q. One-pot diagnostic methods based on CRISPR/Cas and Argonaute nucleases: strategies and perspectives. Trends Biotechnol 2024:S0167-7799(24)00156-2. [PMID: 39034177 DOI: 10.1016/j.tibtech.2024.06.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 05/27/2024] [Accepted: 06/18/2024] [Indexed: 07/23/2024]
Abstract
CRISPR/Cas and Argonaute (Ago) proteins, which target specific nucleic acid sequences, can be applied as diagnostic tools. Despite high specificity and efficiency, achieving sensitive detection often necessitates a preamplification step that involves opening the lid and multistep operation, which may elevate the risk of contamination and prove inadequate for point-of-care testing. Hence, various one-pot detection strategies have been developed that enable preamplification and sensing in a single operation. We outline the challenges of one-pot detection with Cas and Ago proteins, present several main implementation strategies, and discuss future prospects. This review offers comprehensive insights into this vital field and explores potential improvements to detection methods that will be beneficial for human health.
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Affiliation(s)
- Xingyu Ye
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Haoyang Wu
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jinghan Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jiayi Xiang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yan Feng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Qian Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
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10
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Feng W, Peng H, Zhang H, Weinfeld M, Le XC. A Sensitive Technique Unravels the Kinetics of Activation and Trans-Cleavage of CRISPR-Cas Systems. Angew Chem Int Ed Engl 2024; 63:e202404069. [PMID: 38526321 DOI: 10.1002/anie.202404069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 03/21/2024] [Accepted: 03/25/2024] [Indexed: 03/26/2024]
Abstract
Activation of the CRISPR-Cas13a system requires the formation of a crRNA-Cas13a ribonucleoprotein (RNP) complex and the binding of an RNA activator to the RNP. These two binding processes play a crucial role in the performance of the CRISPR-Cas13a system. However, the binding kinetics remain poorly understood, and a main challenge is the lack of a sensitive method for real-time measurements of the dynamically formed active CRISPR-Cas13a enzyme. We describe here a new method to study the binding kinetics and report the rate constants (kon and koff) and dissociation constant (Kd) for the binding between Cas13a and its activator. The method is able to unravel and quantify the kinetics of binding and cleavage separately, on the basis of measuring the real-time trans-cleavage rates of the CRISPR-Cas system and obtaining the real-time concentrations of the active CRISPR-Cas ternary complex. We further discovered that once activated, the Cas13a system operates at a wide range of temperatures (7-37 °C) with fast trans-cleavage kinetics. The new method and findings are important for diverse applications of the Cas13a system, such as the demonstrated quantification of microRNA at ambient temperatures (e.g., 25 °C).
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Affiliation(s)
- Wei Feng
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Hanyong Peng
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Hongquan Zhang
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Michael Weinfeld
- Cross Cancer Institute and Department of Oncology, University of Alberta, Edmonton, Alberta, T6G 1Z2, Canada
| | - X Chris Le
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
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11
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Pian H, Wang H, Wang H, Li Z. Dual CRISPR/Cas13a Cascade Strand Displacement-Triggered Transcription for Point-of-Care Detection of Plasmodium in Asymptomatic Malaria. Anal Chem 2024; 96:7524-7531. [PMID: 38695755 DOI: 10.1021/acs.analchem.4c00230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2024]
Abstract
Asymptomatic infections of Plasmodium parasites are major obstacles to malaria control and elimination. A sensitive, specific, and user-friendly method is urgently needed for point-of-care (POC) Plasmodium diagnostics in asymptomatic malaria, especially in resource-limited settings. In this work, we present a POC method (termed Cas13a-SDT) based on the cascade sequence recognition and signal amplification of dual Cas13a trans-cleavage and strand displacement-triggered transcription (SDT). Cas13a-SDT not only achieves exceptional specificity in discriminating the target RNA from nontarget RNAs with any cross-interaction but also meets the sensitivity criterion set by the World Health Organization (WHO) for effective malaria detection. Remarkably, this novel method was successfully applied to screen malaria in asymptomatic infections from clinical samples. The proposed method provides a user-friendly and visually interpretable output mode while maintaining high accuracy and reliability comparable to RT-PCR. These excellent features demonstrate the significant potential of Cas13a-SDT for POC diagnosis of Plasmodium infections, laying a vital foundation for advancing malaria control and elimination efforts.
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Affiliation(s)
- Hongru Pian
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Hui Wang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Honghong Wang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Zhengping Li
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
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12
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Li P, Ye Y, Li Y, Xie Z, Ye L, Huang J. A MoS 2 nanosheet-based CRISPR/Cas12a biosensor for efficient miRNA quantification for acute myocardial infarction. Biosens Bioelectron 2024; 251:116129. [PMID: 38364329 DOI: 10.1016/j.bios.2024.116129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 12/20/2023] [Accepted: 02/11/2024] [Indexed: 02/18/2024]
Abstract
Acute myocardial infarction (AMI) represents the leading cause of cardiovascular death worldwide, and it is thus pivotal to develop effective approaches for the timely detection of AMI markers, especially possessing the characteristics of antibody-free, signal amplification, and manipulation convenience. We herein construct a MoS2 nanosheet-powered CRISPR/Cas12a sensing strategy for sensitive determination of miR-499, a superior AMI biomarker to protein markers. The presence of miR-499 at a trace level is able to induce a significantly enhanced fluorescence signal in a DNA-based molecular engineering platform, which consists of CRISPR/Cas12a enzymatic reactions and MoS2 nanosheet-controllable signal reporting components. The MoS2 nanosheets were characterized by using atomic force microscopy (AFM) and transmission electron microscope (TEM). The detection feasibility was verified by using polyacrylamide gel electrophoresis (PAGE) analysis and fluorescence measurements. The detection limit is determined as 381.78 pM with the linear range from 0.1 ⅹ 10-9 to 13.33 ⅹ 10-9 M in a fast manner (about 30 min). Furthermore, miRNA detection in real human serum is also conducted with desirable recovery rates (89.5 %-97.6 %), which may find potential application for the clinic diagnosis. We describe herein the first example of MoS2 nanosheet-based signal amplified fluorescence sensor for effective detection of AMI-related miRNA.
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Affiliation(s)
- Peng Li
- Department of Critical Care Medicine, Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524000, PR China; School of Biomedical Engineering, Southern Medical University, Guangzhou, 510515, PR China
| | - Yu Ye
- Department of Radiology, Huangshi Central Hospital, Affiliated Hospital of Hubei Polytechnic University, Huangshi, 435099, PR China
| | - Yang Li
- Department of Critical Care Medicine, Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524000, PR China; School of Biomedical Engineering, Southern Medical University, Guangzhou, 510515, PR China
| | - Zhuohao Xie
- Department of Critical Care Medicine, Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524000, PR China; School of Biomedical Engineering, Southern Medical University, Guangzhou, 510515, PR China
| | - Lei Ye
- Hubei Yangtze Memory Laboratories, Wuhan, 430205, PR China; School of Integrated Circuit, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, PR China.
| | - Jiahao Huang
- Department of Critical Care Medicine, Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524000, PR China; School of Biomedical Engineering, Southern Medical University, Guangzhou, 510515, PR China.
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13
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Zhu F, Yu H, Zhao Q. CRISPR/Cas12a-Amplified Aptamer Switch Microplate Assay for Small Molecules. Anal Chem 2024; 96:6853-6859. [PMID: 38646918 DOI: 10.1021/acs.analchem.4c01452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
The presence of small molecule contaminants such as mycotoxins and heavy metals in foods and the environment causes a serious threat to human health and huge economic losses. The development of simple, rapid, sensitive, and on-site methods for small molecule pollutant detection is highly demanded. Here, combining the advantages of structure-switchable aptamer-mediated signal conversion and CRISPR/Cas12a-based signal amplification, we developed a CRISPR/Cas12a-amplified aptamer switch assay on a microplate for sensitive small molecule detection. In this assay, a short DNA strand complementary to the aptamer (cDNA) is immobilized on a microplate, which can capture the aptamer-linked active DNA probe (Apt-acDNA) in the sample solution when the target is absent. With the addition of the Cas12a reporter system, the captured Apt-acDNA probes activate Cas12a to indiscriminately cleave fluorescent DNA substrates, producing a high fluorescence signal. When the target is present, the Apt-acDNA probe specifically binds to the target rather than hybridizing with cDNA on the microplate, and the fluorescence signal is reduced. The analytical performance of our method was demonstrated by the detection of two highly toxic pollutants, aflatoxin B1 (AFB1) and cadmium ion (Cd2+), as examples. The assay exhibited good selectivity and high sensitivity, with detection limits of 31 pM AFB1 and 3.9 nM Cd2+. It also allowed the detection of targets in the actual sample matrix. With the general signal conversion strategy, this method can be used to detect other targets by simply changing the aptamer and cDNA, showing potential practical applications in broad fields.
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Affiliation(s)
- Fengxi Zhu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hao Yu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiang Zhao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- School of Environment, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China
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14
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Wang Y, Zheng T, Li X, Wu P. Integrating Recombinase Polymerase Amplification and Photosensitization Colorimetric Detection in One Tube for Fast Screening of C. sakazakii in Formula Milk Powder. Anal Chem 2024; 96:5727-5733. [PMID: 38546834 DOI: 10.1021/acs.analchem.4c01130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/10/2024]
Abstract
Cronobacter sakazakii (C. sakazakii) is a widely existing opportunistic pathogen and thus threatens people with low immunity, especially infants. To prevent the outbreak, a rapid and accurate on-site testing method is required. The current standard culture-based method is time-consuming (3-4 days), while the nucleic acid amplification (PCR)-based detection is mostly carried out in central laboratories. Herein, isothermal recombinase polymerase amplification (RPA) coupled with a photosensitization colorimetric assay (PCA) was adopted for the on-site detection of C. sakazakii in powdered infant formulas (PIFs). The lowest visual detection concentration of C. sakazakii is 800 cfu/mL and 2 cfu/g after 8 h bacteria pre-enrichment. Furthermore, to avoid typical cap opening-resulted aerosol pollution, the PCA reagents were lyophilized onto the cap of the RPA tube (containing lyophilized RPA reagents). After amplification, the tube was subjected to simple shaking to mix the PCA reagents with the amplification products for light-driven color development. Such a one-tube assay offered a lowest concentration of 1000 copies of genomic DNA of C. sakazakii within 1 h. After 8 h of bacterial enrichment, the lowest detecting concentration could be pushed down to 5 cfu/g bacteria in PIF. To facilitate on-site monitoring, a portable, battery-powered PCA device was designed to mount the typical RPA 8-tube strip, and a color analysis cellphone APP was further employed for facile readout.
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Affiliation(s)
- Yanying Wang
- Analytical & Testing Center, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610064, China
| | - Ting Zheng
- Analytical & Testing Center, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610064, China
| | - Xianming Li
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Peng Wu
- Analytical & Testing Center, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610064, China
- School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang 453007, China
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15
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Li X, Dang Z, Tang W, Zhang H, Shao J, Jiang R, Zhang X, Huang F. Detection of Parasites in the Field: The Ever-Innovating CRISPR/Cas12a. BIOSENSORS 2024; 14:145. [PMID: 38534252 DOI: 10.3390/bios14030145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 03/11/2024] [Accepted: 03/12/2024] [Indexed: 03/28/2024]
Abstract
The rapid and accurate identification of parasites is crucial for prompt therapeutic intervention in parasitosis and effective epidemiological surveillance. For accurate and effective clinical diagnosis, it is imperative to develop a nucleic-acid-based diagnostic tool that combines the sensitivity and specificity of nucleic acid amplification tests (NAATs) with the speed, cost-effectiveness, and convenience of isothermal amplification methods. A new nucleic acid detection method, utilizing the clustered regularly interspaced short palindromic repeats (CRISPR)-associated (Cas) nuclease, holds promise in point-of-care testing (POCT). CRISPR/Cas12a is presently employed for the detection of Plasmodium falciparum, Toxoplasma gondii, Schistosoma haematobium, and other parasites in blood, urine, or feces. Compared to traditional assays, the CRISPR assay has demonstrated notable advantages, including comparable sensitivity and specificity, simple observation of reaction results, easy and stable transportation conditions, and low equipment dependence. However, a common issue arises as both amplification and cis-cleavage compete in one-pot assays, leading to an extended reaction time. The use of suboptimal crRNA, light-activated crRNA, and spatial separation can potentially weaken or entirely eliminate the competition between amplification and cis-cleavage. This could lead to enhanced sensitivity and reduced reaction times in one-pot assays. Nevertheless, higher costs and complex pre-test genome extraction have hindered the popularization of CRISPR/Cas12a in POCT.
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Affiliation(s)
- Xin Li
- School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Zhisheng Dang
- National Institute of Parasitic Diseases, Chinese Center for Diseases Control and Prevention (Chinese Center for Tropical Diseases Research), Key Laboratory of Parasite and Vector Biology, National Health Commission of the People's Republic of China (NHC), World Health Organization (WHO) Collaborating Center for Tropical Diseases, National Center for International Research on Tropical Diseases, Shanghai 200025, China
| | - Wenqiang Tang
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa 850002, China
- Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa 850002, China
| | - Haoji Zhang
- School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Jianwei Shao
- School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Rui Jiang
- College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Xu Zhang
- School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Fuqiang Huang
- School of Life Science and Engineering, Foshan University, Foshan 528225, China
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Sun Q, Lin H, Li Y, Yuan L, Li B, Ma Y, Wang H, Deng X, Chen H, Tang S. A photocontrolled one-pot isothermal amplification and CRISPR-Cas12a assay for rapid detection of SARS-CoV-2 Omicron variants. Microbiol Spectr 2024; 12:e0364523. [PMID: 38319081 PMCID: PMC10913417 DOI: 10.1128/spectrum.03645-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Accepted: 01/03/2024] [Indexed: 02/07/2024] Open
Abstract
CRISPR-Cas technology has widely been applied to detect single-nucleotide mutation and is considered as the next generation of molecular diagnostics. We previously reported the combination of nucleic acid amplification (NAA) and CRISPR-Cas12a system to distinguish major severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants. However, the mixture of NAA and CRISPR-Cas12a reagents in one tube could interfere with the efficiency of NAA and CRISPR-Cas12a cleavage, which in turn affects the detection sensitivity. In the current study, we employed a novel photoactivated CRISPR-Cas12a strategy integrated with recombinase polymerase amplification (RPA) to develop one-pot RPA/CRISPR-Cas12a genotyping assay for detecting SARS-CoV-2 Omicron sub-lineages. The new system overcomes the potential inhibition of RPA due to early CRISPR-Cas12a activation and cleavage of the target template in traditional one-pot assay using photocleavable p-RNA, a complementary single-stranded RNA to specifically bind crRNA and precisely block Cas12a activation. The detection can be finished in one tube at 39℃ within 1 h and exhibits a low limit of detection of 30 copies per reaction. Our results demonstrated that the photocontrolled one-pot RPA/CRISPR-Cas12a assay could effectively identify three signature mutations in the spike gene of SARS-CoV-2 Omicron variant, namely, R346T, F486V, and 49X, and distinguish Omicron BA.1, BA.5.2, and BF.7 sub-lineages. Furthermore, the assay achieved a sensitivity of 97.3% and a specificity of 100.0% and showed a concordance of 98.3% with Sanger sequencing results.IMPORTANCEWe successfully developed one-pot recombinase polymerase amplification/CRISPR-Cas12a genotyping assay by adapting photocontrolled CRISPR-Cas technology to optimize the conditions of nucleic acid amplification and CRISPR-Cas12a-mediated detection. This innovative approach was able to quickly distinguish severe acute respiratory syndrome coronavirus 2 Omicron variants and can be readily modified for detecting any nucleic acid mutations. The assay system demonstrates excellent clinical performance, including rapid detection, user-friendly operations, and minimized risk of contamination, which highlights its promising potential as a point-of-care testing for wide applications in resource-limiting settings.
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Affiliation(s)
- Qian Sun
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
| | - Hongqing Lin
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
| | - Yuan Li
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
| | - Liping Yuan
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
| | - Baisheng Li
- Institute of Pathogenic Microbiology, Guangdong Provincial Center for Disease Control and Prevention, Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, China
| | - Yunan Ma
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
| | - Haiying Wang
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
| | - Xiaoling Deng
- Institute of Pathogenic Microbiology, Guangdong Provincial Center for Disease Control and Prevention, Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, China
| | - Hongliang Chen
- Department of Clinical Microbiology Laboratory, Chenzhou No. 1 People’s Hospital, Chenzhou, China
| | - Shixing Tang
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
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17
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Priyanka, Mohan B, Poonia E, Kumar S, Virender, Singh C, Xiong J, Liu X, Pombeiro AJL, Singh G. COVID-19 Virus Structural Details: Optical and Electrochemical Detection. J Fluoresc 2024; 34:479-500. [PMID: 37382834 DOI: 10.1007/s10895-023-03307-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/12/2023] [Indexed: 06/30/2023]
Abstract
The increasing viral species have ruined people's health and the world's economy. Therefore, it is urgent to design bio-responsive materials to provide a vast platform for detecting a different family's passive or active virus. One can design a reactive functional unit for that moiety based on the particular bio-active moieties in viruses. Nanomaterials as optical and electrochemical biosensors have enabled better tools and devices to develop rapid virus detection. Various material science platforms are available for real-time monitoring and detecting COVID-19 and other viral loads. In this review, we discuss the recent advances of nanomaterials in developing the tools for optical and electrochemical sensing COVID-19. In addition, nanomaterials used to detect other human viruses have been studied, providing insights for developing COVID-19 sensing materials. The basic strategies for nanomaterials develop as virus sensors, fabrications, and detection performances are studied. Moreover, the new methods to enhance the virus sensing properties are discussed to provide a gateway for virus detection in variant forms. The study will provide systematic information and working of virus sensors. In addition, the deep discussion of structural properties and signal changes will offer a new gate for researchers to develop new virus sensors for clinical applications.
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Affiliation(s)
- Priyanka
- Department of Chemistry and Centre of Advanced Studies, Panjab University, Chandigarh, 160014, India
| | - Brij Mohan
- Centro de Química Estrutural, Institute of Molecular Sciences, Instituto Superior Técnico, Universidade de Lisboa, Av. RoviscoPais, 1049-001, Lisbon, Portugal.
| | - Ekta Poonia
- Department of Chemistry, Deenbandhu Chhotu Ram University of Science & Technology, Murthal, Sonepat, 131039, Haryana, India
| | - Sandeep Kumar
- School of Science, Harbin Institute of Technology (Shenzhen), Shenzhen, 518055, China
| | - Virender
- Department of Chemistry, Kurukshetra University, Kurukshetra, 136119, Haryana, India
| | - Charan Singh
- Department of Pharmaceutical Sciences, School of Sciences, Hemvati Nandan Bahuguna Garhwal University (A Central University), Srinagar, Uttarakhand, 246174, India
| | - Jichuan Xiong
- Electronic and Optical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, People's Republic of China
| | - Xuefeng Liu
- Electronic and Optical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, People's Republic of China
| | - Armando J L Pombeiro
- Centro de Química Estrutural, Institute of Molecular Sciences, Instituto Superior Técnico, Universidade de Lisboa, Av. RoviscoPais, 1049-001, Lisbon, Portugal
| | - Gurjaspreet Singh
- Department of Chemistry and Centre of Advanced Studies, Panjab University, Chandigarh, 160014, India.
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Ngoc LTN, Lee YC. Current Trends in RNA Virus Detection via Nucleic Acid Isothermal Amplification-Based Platforms. BIOSENSORS 2024; 14:97. [PMID: 38392016 PMCID: PMC10886876 DOI: 10.3390/bios14020097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 02/07/2024] [Accepted: 02/09/2024] [Indexed: 02/24/2024]
Abstract
Ribonucleic acid (RNA) viruses are one of the major classes of pathogens that cause human diseases. The conventional method to detect RNA viruses is real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR), but it has some limitations. It is expensive and time-consuming, with infrastructure and trained personnel requirements. Its high throughput requires sophisticated automation and large-scale infrastructure. Isothermal amplification methods have been explored as an alternative to address these challenges. These methods are rapid, user-friendly, low-cost, can be performed in less specialized settings, and are highly accurate for detecting RNA viruses. Microfluidic technology provides an ideal platform for performing virus diagnostic tests, including sample preparation, immunoassays, and nucleic acid-based assays. Among these techniques, nucleic acid isothermal amplification methods have been widely integrated with microfluidic platforms for RNA virus detection owing to their simplicity, sensitivity, selectivity, and short analysis time. This review summarizes some common isothermal amplification methods for RNA viruses. It also describes commercialized devices and kits that use isothermal amplification techniques for SARS-CoV-2 detection. Furthermore, the most recent applications of isothermal amplification-based microfluidic platforms for RNA virus detection are discussed in this article.
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Affiliation(s)
- Le Thi Nhu Ngoc
- Department of Nano Science and Technology Convergence, Gachon University, 1342 Seongnam-Daero, Sujeong-gu, Seongnam-si 13120, Gyeonggi-do, Republic of Korea
| | - Young-Chul Lee
- Department of BioNano Technology, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si 13120, Gyeonggi-do, Republic of Korea
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19
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Park SY, Trinh KTL, Song YJ, Lee NY. Pipette-free field-deployable molecular diagnostic kit for bimodal visual detection of infectious RNA viruses. Biotechnol J 2024; 19:e2300521. [PMID: 38403439 DOI: 10.1002/biot.202300521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 12/22/2023] [Accepted: 01/08/2024] [Indexed: 02/27/2024]
Abstract
Here, we developed a field-deployable molecular diagnostic kit for the detection of RNA viruses that operates in a pipette-free manner. The kit is composed of acrylic sticks, PCR tubes, and palm-sized three-dimensional(3D)-printed heaters operated by batteries. The kit performs RNA extraction, reverse transcriptase loop-mediated isothermal amplification (RT-LAMP), and visual detection in one kit. An acrylic stick was engraved with one shallow and one deep cylindrical chamber at each end for the insertion of an FTA card and ethidium homodimer-1 (EthD-1), respectively, to perform RNA extraction/purification and bimodal visual detection of the target amplicons. First, an intercalation of EthD-1 into the target DNA initially produces fluorescence upon UV illumination. Next, the addition of a strong oxidant, in this case sodium (meta) periodate (NaIO4 ), produces intense aggregates in the presence of EthD-1-intercalated DNA, realized by electrostatic interaction. In the absence of the target amplicon, no fluorescence or aggregates are observed. Using this kit, two major infectious viruses-severe fever with thrombocytopenia syndrome virus (SFTSV) and severe acute respiratory syndrome coronavirus (SARS-CoV-2)-were successfully detected in 1 h, and the limits of detection (LOD) were approximately 1 virus μL-1 for SFTSV and 103 copies μL-1 for SARS-CoV-2 RNA. The introduced kit is portable, end-user-friendly, and can be operated in a pipette-free manner, paving the way for simple and convenient virus detection in resource-limited settings.
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Affiliation(s)
- So Yeon Park
- Department of BioNano Technology, Gachon University, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - Kieu The Loan Trinh
- BioNano Applications Research Center, Gachon University, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - Yoon-Jae Song
- Department of Life Science, Gachon University, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - Nae Yoon Lee
- Department of BioNano Technology, Gachon University, Seongnam-si, Gyeonggi-do, Republic of Korea
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Liu Y, Yang Y, Wang G, Wang D, Shao PL, Tang J, He T, Zheng J, Hu R, Liu Y, Xu Z, Niu D, Lv J, Yang J, Xiao H, Wu S, He S, Tang Z, Liu Y, Tang M, Jiang X, Yuan J, Dai H, Zhang B. Multiplexed discrimination of SARS-CoV-2 variants via plasmonic-enhanced fluorescence in a portable and automated device. Nat Biomed Eng 2023; 7:1636-1648. [PMID: 37735541 DOI: 10.1038/s41551-023-01092-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 08/17/2023] [Indexed: 09/23/2023]
Abstract
Portable assays for the rapid identification of lineages of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are needed to aid large-scale efforts in monitoring the evolution of the virus. Here we report a multiplexed assay in a microarray format for the detection, via isothermal amplification and plasmonic-gold-enhanced near-infrared fluorescence, of variants of SARS-CoV-2. The assay, which has single-nucleotide specificity for variant discrimination, single-RNA-copy sensitivity and does not require RNA extraction, discriminated 12 lineages of SARS-CoV-2 (in three mutational hotspots of the Spike protein) and detected the virus in nasopharyngeal swabs from 1,034 individuals at 98.8% sensitivity and 100% specificity, with 97.6% concordance with genome sequencing in variant discrimination. We also report a compact, portable and fully automated device integrating the entire swab-to-result workflow and amenable to the point-of-care detection of SARS-CoV-2 variants. Portable, rapid, accurate and multiplexed assays for the detection of SARS-CoV-2 variants and lineages may facilitate variant-surveillance efforts.
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Affiliation(s)
- Ying Liu
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Yang Yang
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Infectious Disease Department, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China
| | - Guanghui Wang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Dou Wang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Pan-Lin Shao
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target and Clinical Pharmacology, the NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences and the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Jiahu Tang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Tingzhen He
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Jintao Zheng
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Ruibin Hu
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Yiyi Liu
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Ziyi Xu
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Dan Niu
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Jiahui Lv
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Jingkai Yang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Hongjun Xiao
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Shuai Wu
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Infectious Disease Department, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China
| | - Shuang He
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Zhongrong Tang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Yan Liu
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Infectious Disease Department, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China
| | | | - Xingyu Jiang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China.
| | - Jing Yuan
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Infectious Disease Department, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China.
| | - Hongjie Dai
- Department of Chemistry, Stanford University, Stanford, CA, USA.
| | - Bo Zhang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China.
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21
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Yigci D, Atçeken N, Yetisen AK, Tasoglu S. Loop-Mediated Isothermal Amplification-Integrated CRISPR Methods for Infectious Disease Diagnosis at Point of Care. ACS OMEGA 2023; 8:43357-43373. [PMID: 38027359 PMCID: PMC10666231 DOI: 10.1021/acsomega.3c04422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 09/26/2023] [Indexed: 12/01/2023]
Abstract
Infectious diseases continue to pose an imminent threat to global public health, leading to high numbers of deaths every year and disproportionately impacting developing countries where access to healthcare is limited. Biological, environmental, and social phenomena, including climate change, globalization, increased population density, and social inequity, contribute to the emergence of novel communicable diseases. Rapid and accurate diagnoses of infectious diseases are essential to preventing the transmission of infectious diseases. Although some commonly used diagnostic technologies provide highly sensitive and specific measurements, limitations including the requirement for complex equipment/infrastructure and refrigeration, the need for trained personnel, long sample processing times, and high cost remain unresolved. To ensure global access to affordable diagnostic methods, loop-mediated isothermal amplification (LAMP) integrated clustered regularly interspaced short palindromic repeat (CRISPR) based pathogen detection has emerged as a promising technology. Here, LAMP-integrated CRISPR-based nucleic acid detection methods are discussed in point-of-care (PoC) pathogen detection platforms, and current limitations and future directions are also identified.
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Affiliation(s)
- Defne Yigci
- School
of Medicine, Koç University, Istanbul 34450, Turkey
| | - Nazente Atçeken
- Koç
University Translational Medicine Research Center (KUTTAM), Koç University, Istanbul 34450, Turkey
| | - Ali K. Yetisen
- Department
of Chemical Engineering, Imperial College
London, London SW7 2AZ, U.K.
| | - Savas Tasoglu
- Koç
University Translational Medicine Research Center (KUTTAM), Koç University, Istanbul 34450, Turkey
- Boğaziçi
Institute of Biomedical Engineering, Boğaziçi
University, Istanbul 34684, Turkey
- Koç
University Arçelik Research Center for Creative Industries
(KUAR), Koç University, Istanbul 34450, Turkey
- Physical
Intelligence Department, Max Planck Institute
for Intelligent Systems, Stuttgart 70569, Germany
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22
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Zhang M, Wang H, Han J, Wang H, Jia Y, Hong W, Tang F, Li Z. Specific recognition and sensitive quantification of mRNA splice variants via one-pot ligation-dependent loop-mediated isothermal amplification. Analyst 2023; 148:5605-5611. [PMID: 37818948 DOI: 10.1039/d3an01382k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Specific recognition and sensitive quantification of mRNA alternative splice variants have been a necessity for exploring the regulatory mechanism of RNA splicing and revealing the association between pre-mRNA splicing and transcriptome function, as well as disease diagnosis. However, their wide abundance range and high sequence homology pose enormous challenges for high sensitivity and selectivity quantification of splice variants. Herein, taking advantage of the excellent specificity of ligation and the powerful nucleic acid replication feature of loop-mediated isothermal amplification (LAMP), we developed a one-pot method (termed one-pot ligation-LAMP) for specific recognition and sensitive quantification of mRNA splicing variants based on two splicing junction-specific stem-loop DNA probe ligation and the subsequently initiating LAMP. The one-pot ligation-LAMP can specifically detect as low as 100 aM mRNA splice variants without any nonspecific signals and quantify them with a wide dynamics range spanning at least six orders of magnitude. We have demonstrated that the one-pot ligation-LAMP is a versatile and practical strategy for accurately quantifying different splicing variants in complex biological samples with high sensitivity all in one tube within 90 min, thereby providing an attractive tool for mRNA splice variant-related studies.
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Affiliation(s)
- Mai Zhang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China.
| | - Hui Wang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China.
| | - Jun Han
- National Textile and Leather Product Quality Inspection and Testing Centre, 15 Xili-Balizhuang, Chaoyang District, Beijing 100025, China
| | - Honghong Wang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China.
| | - Yuting Jia
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China.
| | - Weixiang Hong
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China.
| | - Fu Tang
- School of Materials Science and Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Zhengping Li
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China.
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23
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Wang B, Yang H. Progress of CRISPR-based programmable RNA manipulation and detection. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1804. [PMID: 37282821 DOI: 10.1002/wrna.1804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 05/09/2023] [Accepted: 05/12/2023] [Indexed: 06/08/2023]
Abstract
Prokaryotic clustered regularly interspaced short palindromic repeats and CRISPR associated (CRISPR-Cas) systems provide adaptive immunity by using RNA-guided endonucleases to recognize and eliminate invading foreign nucleic acids. Type II Cas9, type V Cas12, type VI Cas13, and type III Csm/Cmr complexes have been well characterized and developed as programmable platforms for selectively targeting and manipulating RNA molecules of interest in prokaryotic and eukaryotic cells. These Cas effectors exhibit remarkable diversity of ribonucleoprotein (RNP) composition, target recognition and cleavage mechanisms, and self discrimination mechanisms, which are leveraged for various RNA targeting applications. Here, we summarize the current understanding of mechanistic and functional characteristics of these Cas effectors, give an overview on RNA detection and manipulation toolbox established so far including knockdown, editing, imaging, modification, and mapping RNA-protein interactions, and discuss the future directions for CRISPR-based RNA targeting tools. This article is categorized under: RNA Methods > RNA Analyses in Cells RNA Processing > RNA Editing and Modification RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Beibei Wang
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Hui Yang
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
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24
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Deng Z, Zhou J, Wang C, Hu J, Liu R, Lv Y. Rapid and sensitive point-of-care PTS-CRISPR assay for food safety monitoring of aflatoxin B1. Chem Commun (Camb) 2023; 59:12011-12014. [PMID: 37727951 DOI: 10.1039/d3cc03984f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/21/2023]
Abstract
Food safety is crucial for human health, but its effective on-site monitoring remains a challenge. Pregnancy test strip (PTS) is the successful point-of-care testing (POCT) product of the highest market share in the world, with the cost as low as $0.10 per test. Herein, combined with the CRISPR (clustered regularly interspaced short palindromic repeats) system, PTS-CRISPR was for the first time introduced into food safety monitoring, for rapid and sensitive POCT of aflatoxin B1. The low-cost, easy-to-operate PTS-CRISPR is expected to bring security to the grassroots food market.
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Affiliation(s)
- Ziqiang Deng
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064, China.
| | - Jin Zhou
- Analytical & Testing Centre, Sichuan University, Chengdu 610064, China.
| | - Chaoqun Wang
- Analytical & Testing Centre, Sichuan University, Chengdu 610064, China.
| | - Jianyu Hu
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
| | - Rui Liu
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064, China.
| | - Yi Lv
- Analytical & Testing Centre, Sichuan University, Chengdu 610064, China.
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25
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Zhou S, Zhu S, Huang Z, Chen J, Li J, Yang M, Jin L, Huo D, Hou C. Target-mediated rolling circle transcription coupling with CRISPR/Cas12a-Cas13a for simultaneous detection of HPV16 and HPV18. Chem Commun (Camb) 2023; 59:11987-11990. [PMID: 37727048 DOI: 10.1039/d3cc04223e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/21/2023]
Abstract
Simultaneous detection of multiple targets can provide important data support for clinical diagnosis and treatment. Here, we report a facile isothermal assay based on target-mediated rolling circle transcription coupling with CRISPR/Cas12a-Cas13a (TM-RCT/Cas12a-Cas13a). Through facile one-step amplification (TM-RCT), two target DNAs are converted to RNA amplified products. The simultaneous detection of HPV16 and HPV18 is then achieved by combining two CRISPR/Cas systems. This system shows excellent sensing performance and provides a universal method for simultaneous detection.
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Affiliation(s)
- Shiying Zhou
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing 400044, PR China
| | - Shuyu Zhu
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing 400044, PR China
| | - Zhen Huang
- Key Laboratory of Bio-Resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, SeNA Research Institute and Szostak-CDHT Large Nucleic Acids Institute, Chengdu, 610000, PR China
| | - Jian Chen
- Chongqing University Three Gorges Hospital, Chongqing, 404000, PR China
| | - Jiawei Li
- Chongqing University Three Gorges Hospital, Chongqing, 404000, PR China
| | - Mei Yang
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing 400044, PR China
| | - Liang Jin
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing 400044, PR China
| | - Danqun Huo
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing 400044, PR China
| | - Changjun Hou
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing 400044, PR China
- Chongqing Key Laboratory of Bio-perception & Intelligent Information Processing, School of Microelectronics and Communication Engineering, Chongqing University, Chongqing, 400044, PR China.
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26
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Liu H, Hu X, Zeng H, He C, Cheng F, Tang X, Wang J. A rapid and high-throughput system for the detection of transgenic products based on LAMP-CRISPR-Cas12a. Curr Res Food Sci 2023; 7:100605. [PMID: 37868002 PMCID: PMC10589767 DOI: 10.1016/j.crfs.2023.100605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 09/21/2023] [Accepted: 09/25/2023] [Indexed: 10/24/2023] Open
Abstract
With the increasing acreage of genetically modified crops worldwide, rapid and efficient detection technologies have become very important for the regulation and screening of GM organisms. We constructed a method based on loop-mediated isothermal amplification (LAMP), CRISPR-Cas12a and lateral flow assay (LAMP-CRISPR-Cas12a-LFA). It is an intuitive, sensitive and specific fluorescence detection and test strip system to detect CP4-EPSPS and Cry1Ab/Ac genes in field screening. The LAMP-CRISPR-Cas12a-LFA method has a limit of detection (LOD) of 100 copies based on lateral flow test strips after optimization of the conditions with screened specific primers, and the entire detection process can be completed within 1 h at 61 °C. The system was used to evaluate field test samples and showed high reproducibility after testing products containing CP4-EPSPS and Cry1Ab/Ac genes, and both were detectable. The LAMP-CRISPR-Cas12a-LFA method established in this paper functions as a rapid field detection method. It requires only one portable thermostatic instrument, which renders it compatible with the rapid detection of field samples and useable at experimental workstations, in law enforcement field work, and in local inspection and quarantine departments.
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Affiliation(s)
- Hua Liu
- Institute of Biotechnology Research, Shanghai Academy of Agricultural Sciences, Key Laboratory of Agricultural Genetics and Breeding, 2901 Beidi Road, Shanghai, 201106, China
| | - Xiuwen Hu
- College of Food Sciences and Technology, Shanghai Ocean University, 999 Huancheng Road Shanghai, 200120, China
| | - Haijuan Zeng
- Institute of Biotechnology Research, Shanghai Academy of Agricultural Sciences, Key Laboratory of Agricultural Genetics and Breeding, 2901 Beidi Road, Shanghai, 201106, China
| | - Chuan He
- Institute of Biotechnology Research, Shanghai Academy of Agricultural Sciences, Key Laboratory of Agricultural Genetics and Breeding, 2901 Beidi Road, Shanghai, 201106, China
| | - Fang Cheng
- Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xueming Tang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jinbin Wang
- Institute of Biotechnology Research, Shanghai Academy of Agricultural Sciences, Key Laboratory of Agricultural Genetics and Breeding, 2901 Beidi Road, Shanghai, 201106, China
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27
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Sharma N, Neill T, Yang HC, Oliver CL, Mahaffee WF, Naegele R, Moyer MM, Miles TD. Development of a PNA-LNA-LAMP Assay to Detect an SNP Associated with QoI Resistance in Erysiphe necator. PLANT DISEASE 2023; 107:3238-3247. [PMID: 37005502 DOI: 10.1094/pdis-09-22-2027-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
The repetitive use of quinone outside inhibitor fungicides (QoIs, strobilurins; Fungicide Resistance Action Committee [FRAC] 11) to manage grape powdery mildew has led to development of resistance in Erysiphe necator. While several point mutations in the mitochondrial cytochrome b gene are associated with resistance to QoI fungicides, the substitution of glycine to alanine at codon 143 (G143A) has been the only mutation observed in QoI-resistant field populations. Allele-specific detection methods such as digital droplet PCR and TaqMan probe-based assays can be used to detect the G143A mutation. In this study, a peptide nucleic acid-locked nucleic acid mediated loop-mediated isothermal amplification (PNA-LNA-LAMP) assay consisting of an A-143 reaction and a G-143 reaction, was designed for rapidly detecting QoI resistance in E. necator. The A-143 reaction amplifies the mutant A-143 allele faster than the wild-type G-143 allele, while the G-143 reaction amplifies the G-143 allele faster than the A-143 allele. Identification of resistant or sensitive E. necator samples was determined by which reaction had the shorter time to amplification. Sixteen single-spore QoI-resistant and -sensitive E. necator isolates were tested using both assays. Assay specificity in distinguishing the single nucleotide polymorphism (SNP) approached 100% when tested using purified DNA of QoI-sensitive and -resistant E. necator isolates. This diagnostic tool was sensitive to one-conidium equivalent of extracted DNA with an R2 value of 0.82 and 0.87 for the G-143 and A-143 reactions, respectively. This diagnostic approach was also evaluated against a TaqMan probe-based assay using 92 E. necator samples collected from vineyards. The PNA-LNA-LAMP assay detected QoI resistance in ≤30 min and showed 100% agreement with the TaqMan probe-based assay (≤1.5 h) for the QoI-sensitive and -resistant isolates. There was 73.3% agreement with the TaqMan probe-based assay when samples had mixed populations with both G-143 and A-143 alleles present. Validation of the PNA-LNA-LAMP assay was conducted in three different laboratories with different equipment. The results showed 94.4% accuracy in one laboratory and 100% accuracy in two other laboratories. The PNA-LNA-LAMP diagnostic tool was faster and required less expensive equipment relative to the previously developed TaqMan probe-based assay, making it accessible to a broader range of diagnostic laboratories for detection of QoI resistance in E. necator. This research demonstrates the utility of the PNA-LANA-LAMP for discriminating SNPs from field samples and its utility for point-of-care monitoring of plant pathogen genotypes.
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Affiliation(s)
- Nancy Sharma
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI
| | - Tara Neill
- USDA-ARS Horticultural Crops Disease and Pest Management Research Unit, Corvallis, OR
| | - Hui-Ching Yang
- USDA-ARS Crop Diseases, Pests and Genetics Unit, San Joaquin Valley Agricultural Sciences Center, Parlier, CA
| | - Charlotte L Oliver
- Department of Horticulture, Irrigated Agriculture Research and Extension Center, Washington State University, Prosser, WA
| | - Walter F Mahaffee
- USDA-ARS Horticultural Crops Disease and Pest Management Research Unit, Corvallis, OR
| | - Rachel Naegele
- USDA-ARS Crop Diseases, Pests and Genetics Unit, San Joaquin Valley Agricultural Sciences Center, Parlier, CA
| | - Michelle M Moyer
- Department of Horticulture, Irrigated Agriculture Research and Extension Center, Washington State University, Prosser, WA
| | - Timothy D Miles
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI
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28
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Nguyen T, Vinayaka AC, Huynh VN, Linh QT, Andreasen SZ, Golabi M, Bang DD, Møller JK, Wolff A. PATHPOD - A loop-mediated isothermal amplification (LAMP)-based point-of-care system for rapid clinical detection of SARS-CoV-2 in hospitals in Denmark. SENSORS AND ACTUATORS. B, CHEMICAL 2023; 392:134085. [PMID: 37304211 PMCID: PMC10245468 DOI: 10.1016/j.snb.2023.134085] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 05/19/2023] [Accepted: 06/03/2023] [Indexed: 06/13/2023]
Abstract
Sensitive and rapid detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been a vital goal in the ongoing COVID-19 pandemic. We present in this comprehensive work, for the first time, detailed fabrication and clinical validation of a point of care (PoC) device for rapid, onsite detection of SARS-CoV-2 using a real-time reverse-transcription loop-mediated isothermal amplification (RT-LAMP) reaction on a polymer cartridge. The PoC system, namely PATHPOD, consisting of a standalone device (weight less than 1.2 kg) and a cartridge, can perform the detection of 10 different samples and two controls in less than 50 min, which is much more rapid than the golden standard real-time reverse-transcription Polymerase Chain Reaction (RT-PCR), typically taking 16-48 h. The novel total internal reflection (TIR) scheme and the reactions inside the cartridge in the PoC device allow monitoring of the diagnostic results in real-time and onsite. The analytical sensitivity and specificity of the PoC test are comparable with the current RT-PCR, with a limit of detection (LOD) down to 30-50 viral genome copies. The robustness of the PATHPOD PoC system has been confirmed by analyzing 398 clinical samples initially examined in two hospitals in Denmark. The clinical sensitivity and specificity of these tests are discussed.
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Affiliation(s)
- Trieu Nguyen
- BioLabChip Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Aaydha Chidambara Vinayaka
- Laboratory of Applied Micro and Nanotechnology (LAMINATE), Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Van Ngoc Huynh
- BioLabChip Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Quyen Than Linh
- BioLabChip Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Sune Zoëga Andreasen
- BioLabChip Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Mohsen Golabi
- Laboratory of Applied Micro and Nanotechnology (LAMINATE), Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Dang Duong Bang
- Laboratory of Applied Micro and Nanotechnology (LAMINATE), Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Jens Kjølseth Møller
- Department of Clinical Microbiology, University Hospital of Southern Denmark, Vejle Hospital, Beriderbakken 4, DK-7100 Vejle, Denmark
| | - Anders Wolff
- BioLabChip Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
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29
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Jiang L, Lan X, Ren L, Jin Z, Shan X, Yang M, Chang L. Single-molecule RNA capture-assisted droplet digital loop-mediated isothermal amplification for ultrasensitive and rapid detection of infectious pathogens. MICROSYSTEMS & NANOENGINEERING 2023; 9:118. [PMID: 37767528 PMCID: PMC10519972 DOI: 10.1038/s41378-023-00576-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 05/27/2023] [Accepted: 06/16/2023] [Indexed: 09/29/2023]
Abstract
To minimize and control the transmission of infectious diseases, a sensitive, accurate, rapid, and robust assay strategy for application on-site screening is critical. Here, we report single-molecule RNA capture-assisted digital RT-LAMP (SCADL) for point-of-care testing of infectious diseases. Target RNA was captured and enriched by specific capture probes and oligonucleotide probes conjugated to magnetic beads, replacing laborious RNA extraction. Droplet generation, amplification, and the recording of results are all integrated on a microfluidic chip. In assaying commercial standard samples, quantitative results precisely corresponded to the actual concentration of samples. This method provides a limit of detection of 10 copies mL-1 for the N gene within 1 h, greatly reducing the need for skilled personnel and precision instruments. The ultrasensitivity, specificity, portability, rapidity and user-friendliness make SCADL a competitive candidate for the on-site screening of infectious diseases.
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Affiliation(s)
- Liying Jiang
- School of Electrical and Information Engineering, Zhengzhou University of Light Industry, 450002 Zhengzhou, China
- Academy for Quantum Science and Technology, Zhengzhou University of Light Industry, 450002 Zhengzhou, China
| | - Xianghao Lan
- School of Electrical and Information Engineering, Zhengzhou University of Light Industry, 450002 Zhengzhou, China
| | - Linjiao Ren
- School of Electrical and Information Engineering, Zhengzhou University of Light Industry, 450002 Zhengzhou, China
| | - Zhiyuan Jin
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, 100191 Beijing, China
| | - Xuchen Shan
- School of Physics, Beihang University, 100191 Beijing, China
| | - Mingzhu Yang
- Beijing Research Institute of Mechanical Equipment, 100143 Beijing, China
| | - Lingqian Chang
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, 100191 Beijing, China
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30
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Li X, Zhong J, Li H, Qiao Y, Mao X, Fan H, Zhong Y, Imani S, Zheng S, Li J. Advances in the application of CRISPR-Cas technology in rapid detection of pathogen nucleic acid. Front Mol Biosci 2023; 10:1260883. [PMID: 37808520 PMCID: PMC10552857 DOI: 10.3389/fmolb.2023.1260883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 09/06/2023] [Indexed: 10/10/2023] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated proteins (Cas) are widely used as gene editing tools in biology, microbiology, and other fields. CRISPR is composed of highly conserved repetitive sequences and spacer sequences in tandem. The spacer sequence has homology with foreign nucleic acids such as viruses and plasmids; Cas effector proteins have endonucleases, and become a hotspot in the field of molecular diagnosis because they recognize and cut specific DNA or RNA sequences. Researchers have developed many diagnostic platforms with high sensitivity, high specificity, and low cost by using Cas proteins (Cas9, Cas12, Cas13, Cas14, etc.) in combination with signal amplification and transformation technologies (fluorescence method, lateral flow technology, etc.), providing a new way for rapid detection of pathogen nucleic acid. This paper introduces the biological mechanism and classification of CRISPR-Cas technology, summarizes the existing rapid detection technology for pathogen nucleic acid based on the trans cleavage activity of Cas, describes its characteristics, functions, and application scenarios, and prospects the future application of this technology.
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Affiliation(s)
- Xiaoping Li
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
- Faculty of Medicine, Macau University of Science and Technology, Avenida Wai Long Taipa, Macau, China
| | - Jiaye Zhong
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Haoyu Li
- NHC Key Laboratory of Combined Multi-Organ Transplantation, Hangzhou, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
| | - Yinbiao Qiao
- Department of Hepatobiliary and Pancreatic Surgery, Department of Liver Transplantation, Shulan (Hangzhou) Hospital, Zhejiang Shuren University School of Medicine, Hangzhou, China
- NHC Key Laboratory of Combined Multi-Organ Transplantation, Hangzhou, China
| | - Xiaolei Mao
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Huayan Fan
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Yiwu Zhong
- Zhejiang Chinese Medical University, Hangzhou, China
| | - Saber Imani
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Shusen Zheng
- Department of Hepatobiliary and Pancreatic Surgery, Department of Liver Transplantation, Shulan (Hangzhou) Hospital, Zhejiang Shuren University School of Medicine, Hangzhou, China
- NHC Key Laboratory of Combined Multi-Organ Transplantation, Hangzhou, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
| | - Jianhui Li
- Department of Hepatobiliary and Pancreatic Surgery, Department of Liver Transplantation, Shulan (Hangzhou) Hospital, Zhejiang Shuren University School of Medicine, Hangzhou, China
- NHC Key Laboratory of Combined Multi-Organ Transplantation, Hangzhou, China
- The Organ Repair and Regeneration Medicine Institute of Hangzhou, Hangzhou, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
- Zhejiang Chinese Medical University, Hangzhou, China
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31
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Wei J, Wang W, Yu Q, Zhang M, Xue F, Fan B, Zhang T, Gao Y, Li J, Meng X, Pang B. MASTR Pouch: Palm-size lab for point-of-care detection of Mpox using recombinase polymerase amplification and CRISPR technology. SENSORS AND ACTUATORS. B, CHEMICAL 2023; 390:133950. [PMID: 37193119 PMCID: PMC10164292 DOI: 10.1016/j.snb.2023.133950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/18/2023] [Accepted: 05/06/2023] [Indexed: 05/18/2023]
Abstract
Mpox (formerly referred as Monkeypox) outbreak has been declared a Public Health Emergency of International Concern. However, traditional polymerase chain reaction (PCR) diagnostic technology is not ideal for on-site applications. To conduct the sample-to-result Mpox viral particles detection outside the laboratories, we developed an easy-to-operate palm-size pouch, termed Mpox At-home Self-Test and point-of-caRe Pouch (MASTR Pouch). In this MASTR Pouch, the fast and accurate visualization was achieved by incorporating recombinase polymerase amplification (RPA) with clustered regularly interspaced short palindromic repeat (CRISPR)/Cas12a system. From viral particle lysis to naked eye readout, MASTR Pouch required only four simple steps to accomplish the analysis process within 35 min. Fifty-three Mpox pseudo-viral particles in exudate (10.6 particles/μL) were able to be detected. To verify the practicability, 104 mock Mpox clinical exudate specimens were tested. The clinical sensitivities were determined to be 91.7%- 95.8%. There was no false-positive result, validating the 100% clinical specificity. MASTR Pouch approaches the WHO's ASSURD criteria for point-of-care diagnostic, which will be beneficial for mitigating Mpox's global spread. The versatility potential of MASTR Pouch could further revolutionize infection diagnosis.
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Affiliation(s)
- Jia Wei
- Department of Thyroid Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun, Jilin 130021, PR China
| | - Wanjun Wang
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangzhou 510006, PR China
- School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, PR China
| | - Qiong Yu
- School of Public Health, Jilin University, Changchun 130021, PR China
| | - Mingrui Zhang
- Department of Dermatology, The Second Hospital of Jilin University, Changchun 130000, PR China
| | - Fengyu Xue
- School of Public Health, Jilin University, Changchun 130021, PR China
| | - Beibei Fan
- School of Public Health, Jilin University, Changchun 130021, PR China
| | - Tong Zhang
- State Key Laboratory of Integrated Optoelectronics, College of Electronic Science and Engineering, Jilin University, Changchun 130012, PR China
| | - Yanpeng Gao
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangzhou 510006, PR China
- School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, PR China
| | - Juan Li
- School of Public Health, Jilin University, Changchun 130021, PR China
| | - Xianying Meng
- Department of Thyroid Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun, Jilin 130021, PR China
| | - Bo Pang
- School of Public Health, Jilin University, Changchun 130021, PR China
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Alipanah M, Manzanas C, Hai X, Lednicky JA, Paniz-Mondolfi A, Morris JG, Fan ZH. Mayaro virus detection by integrating sample preparation with isothermal amplification in portable devices. Anal Bioanal Chem 2023; 415:5605-5617. [PMID: 37470813 PMCID: PMC10528734 DOI: 10.1007/s00216-023-04856-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 07/04/2023] [Accepted: 07/06/2023] [Indexed: 07/21/2023]
Abstract
Mayaro virus (MAYV) is an emerging mosquito-borne alphavirus that causes clinical symptoms similar to those caused by Chikungunya virus (CHIKV), Dengue virus (DENV), and Zika virus (ZIKV). To differentiate MAYV from these viruses diagnostically, we have developed a portable device that integrates sample preparation with real-time, reverse-transcription, loop-mediated isothermal amplification (rRT-LAMP). First, we designed a rRT-LAMP assay targeting MAYV's non-structural protein (NS1) gene and determined the limit of detection of at least 10 viral genome equivalents per reaction. The assay was specific for MAYV, without cross-reactions with CHIKV, DENV, or ZIKV. The rRT-LAMP assay was integrated with a sample preparation device (SPD) wherein virus lysis and RNA enrichment/purification were carried out on the spot, without requiring pipetting, while subsequent real-time amplification device (RAD) enables virus detection at the point of care (POC). The functions of our platform were demonstrated using purified MAYV RNA or blood samples containing viable viruses. We have used the devices for detection of MAYV in as short as 13 min, with limit of detection to as low as 10 GEs/reaction.
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Affiliation(s)
- Morteza Alipanah
- Interdisciplinary Microsystems Group, Department of Mechanical and Aerospace Engineering, University of Florida, P.O. Box 116250, Gainesville, FL, 32611, USA
| | - Carlos Manzanas
- Interdisciplinary Microsystems Group, Department of Mechanical and Aerospace Engineering, University of Florida, P.O. Box 116250, Gainesville, FL, 32611, USA
| | - Xin Hai
- Interdisciplinary Microsystems Group, Department of Mechanical and Aerospace Engineering, University of Florida, P.O. Box 116250, Gainesville, FL, 32611, USA
| | - John A Lednicky
- Emerging Pathogens Institute, University of Florida, P.O. Box 100009, Gainesville, FL, 32610, USA.
- Department of Environmental and Global Health, University of Florida, PO Box 100188, Gainesville, FL, 32610, USA.
| | - Alberto Paniz-Mondolfi
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, New York, NY, 10029, USA
| | - J Glenn Morris
- Emerging Pathogens Institute, University of Florida, P.O. Box 100009, Gainesville, FL, 32610, USA
| | - Z Hugh Fan
- Interdisciplinary Microsystems Group, Department of Mechanical and Aerospace Engineering, University of Florida, P.O. Box 116250, Gainesville, FL, 32611, USA.
- Emerging Pathogens Institute, University of Florida, P.O. Box 100009, Gainesville, FL, 32610, USA.
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, P.O. Box 116131, Gainesville, FL, 32611, USA.
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, FL, 32611, USA.
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Curtin K, Wang J, Fike BJ, Binkley B, Li P. A 3D printed microfluidic device for scalable multiplexed CRISPR-cas12a biosensing. Biomed Microdevices 2023; 25:34. [PMID: 37642743 DOI: 10.1007/s10544-023-00675-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/11/2023] [Indexed: 08/31/2023]
Abstract
Accurate, rapid, and multiplexed nucleic acid detection is critical for environmental and biomedical monitoring. In recent years, CRISPR-Cas12a has shown great potential in improving the performance of DNA biosensing. However, the nonspecific trans-cleavage activity of Cas12a complicates the multiplexing capability of Cas12a biosensing. We report a 3D-printed composable microfluidic plate (cPlate) device that utilizes miniaturized wells and microfluidic loading for a multiplexed CRISPR-Cas12a assay. The device easily combines loop-mediated isothermal amplification (LAMP) and CRISPR-Cas12a readout in a simple and high-throughput workflow with low reagent consumption. To ensure the maximum performance of the device, the concentration of Cas12a and detection probe was optimized, which yielded a four-fold sensitivity improvement. Our device demonstrates sensitive detection to the fg mL- 1 level for four waterborne pathogens including shigella, campylobacter, cholera, and legionella within 1 h, making it suitable for low-resource settings.
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Affiliation(s)
- Kathrine Curtin
- Department of Mechanical and Aerospace Engineering, West Virginia University, Morgantown, WV, USA
| | - Jing Wang
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Bethany J Fike
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Brandi Binkley
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Peng Li
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA.
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Tian T, Zhou X. CRISPR-Based Biosensing Strategies: Technical Development and Application Prospects. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2023; 16:311-332. [PMID: 37018798 DOI: 10.1146/annurev-anchem-090822-014725] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Biosensing based on CRISPR-Cas systems is a young but rapidly evolving technology. The unprecedented properties of the CRISPR-Cas system provide an innovative tool for developing new-generation biosensing strategies. To date, a series of nucleic acid and non-nucleic acid detection methods have been developed based on the CRISPR platform. In this review, we first introduce the core biochemical properties underpinning the development of CRISPR bioassays, such as diverse reaction temperatures, programmability in design, high reaction efficiency, and recognition specificity, and highlight recent efforts to improve these parameters. We then introduce the technical developments, including how to improve sensitivity and quantification capabilities, develop multiplex assays, achieve convenient one-pot assays, create advanced sensors, and extend the applications of detection. Finally, we analyze obstacles to the commercial application of CRISPR detection technology and explore development opportunities and directions.
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Affiliation(s)
- Tian Tian
- School of Life Sciences, South China Normal University, Guangzhou, China;
| | - Xiaoming Zhou
- School of Life Sciences, South China Normal University, Guangzhou, China;
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Fan Z, Mei Y, Xing J, Chen T, Hu D, Liu H, Li Y, Liu D, Liu Z, Liang Y. Loop-mediated isothermal amplification (LAMP)/Cas12a assay for detection of Ralstonia solanacearum in tomato. Front Bioeng Biotechnol 2023; 11:1188176. [PMID: 37284238 PMCID: PMC10239818 DOI: 10.3389/fbioe.2023.1188176] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 05/11/2023] [Indexed: 06/08/2023] Open
Abstract
Introduction: Bacterial wilt (BW) caused by the aerobic, Gram-negative pathogenic species Ralstonia solanacearum (RS) is a major disease impacting commercial agriculture worldwide. Asian phylotype I of RS is the cause of tomato bacterial wilt, which has caused severe economic losses in southern China for many years. An urgent priority in control of bacterial wilt is development of rapid, sensitive, effective methods for detection of RS. Methods: We describe here a novel RS detection assay based on combination of loop-mediated isothermal amplification (LAMP) and CRISPR/Cas12a. crRNA1, with high trans-cleavage activity targeting hrpB gene, was selected out of four candidate crRNAs. Two visual detection techniques, involving naked-eye observation of fluorescence and lateral flow strips, were tested and displayed high sensitivity and strong specificity. Results and Discussion: The LAMP/Cas12a assay accurately detected RS phylotype Ⅰ in 14 test strains, and showed low detection limit (2.0 × 100 copies). RS in tomato stem tissue and soil samples from two field sites with suspected BW infection was identified accurately, suggesting potential application of LAMP/Cas12a assay as point-of-care test (POCT). The overall detection process took less than 2 h and did not require professional lab equipment. Our findings, taken together, indicate that LAMP/Cas12a assay can be developed as an effective, inexpensive technique for field detection and monitoring of RS.
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Affiliation(s)
- Zhiyu Fan
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yuxia Mei
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jiawei Xing
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Tian Chen
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Di Hu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Hui Liu
- GNSS Research Center, Wuhan University, Wuhan, China
| | - Yingjun Li
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Derui Liu
- Hubei Jiamachi Ecological Agriculture Co, Ltd, Yichang, China
- Hubei Yishizhuang Agricultural Technology Co, Ltd, Yichang, China
| | - Zufeng Liu
- Hubei Jiamachi Ecological Agriculture Co, Ltd, Yichang, China
- Hubei Yishizhuang Agricultural Technology Co, Ltd, Yichang, China
| | - Yunxiang Liang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
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Yang X, Zeng X, Chen X, Huang J, Wei X, Ying X, Tan Q, Wang Y, Li S. Development of a CRISPR/Cas12a-recombinase polymerase amplification assay for visual and highly specific identification of the Congo Basin and West African strains of mpox virus. J Med Virol 2023; 95:e28757. [PMID: 37212293 DOI: 10.1002/jmv.28757] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 03/27/2023] [Accepted: 04/13/2023] [Indexed: 05/23/2023]
Abstract
Human mpox is a zoonotic disease, similar to smallpox, caused by the mpox virus, which is further subdivided into Congo Basin and West African clades with different pathogenicity. In this study, a novel diagnostic protocol utilizing clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 12a nuclease (CRISPR/Cas12a)-mediated recombinase polymerase amplification (RPA) was developed to identify mpox in the Congo Basin and West Africa (CRISPR-RPA). Specific RPA primers targeting D14L and ATI were designed. CRISPR-RPA assay was performed using various target templates. In the designed CRISPR-RPA reaction system, the exponentially amplified RPA amplification products with a protospacer adjacent motif (PAM) site can locate the Cas12a/crRNA complex to its target regions, which successfully activates the CRISPR/Cas12a effector and achieves ultrafast trans-cleavage of a single-stranded DNA probe. The limit of detection for the CRISPR-RPA assay was 10 copies per reaction for D14L- and ATI-plasmids. No cross-reactivity was observed with non-mpox strains, confirming the high specificity of the CRISPR-RPA assay for distinguishing between the Congo Basin and West African mpox. The CRISPR-RPA assay can be completed within 45 min using real-time fluorescence readout. Moreover, the cleavage results were visualized under UV light or an imaging system, eliminating the need for a specialized apparatus. In summary, the developed CRISPR/RPA assay is a visual, rapid, sensitive, and highly specific detection technique that can be used as an attractive potential identification tool for Congo Basin and West African mpox in resource-limited laboratories.
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Affiliation(s)
- Xinggui Yang
- Guizhou Provincial Center for Disease Control and Prevention, Guiyang, Guizhou, P.R. China
| | - Xiaoyan Zeng
- The Second Affiliated Hospital, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, P.R. China
| | - Xu Chen
- The Second Affiliated Hospital, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, P.R. China
| | - Junfei Huang
- Guizhou Provincial Center for Disease Control and Prevention, Guiyang, Guizhou, P.R. China
| | - Xiaoyu Wei
- Guizhou Provincial Center for Disease Control and Prevention, Guiyang, Guizhou, P.R. China
| | - Xia Ying
- Guizhou Provincial Center for Disease Control and Prevention, Guiyang, Guizhou, P.R. China
| | - Qinqin Tan
- Guizhou Provincial Center for Disease Control and Prevention, Guiyang, Guizhou, P.R. China
| | - Yi Wang
- Experimental Research Center, Capital Institute of Pediatrics, Beijing, P.R. China
| | - Shijun Li
- Guizhou Provincial Center for Disease Control and Prevention, Guiyang, Guizhou, P.R. China
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Ansah IB, Leming M, Lee SH, Yang JY, Mun C, Noh K, An T, Lee S, Kim DH, Kim M, Im H, Park SG. Label-free detection and discrimination of respiratory pathogens based on electrochemical synthesis of biomaterials-mediated plasmonic composites and machine learning analysis. Biosens Bioelectron 2023; 227:115178. [PMID: 36867960 PMCID: PMC10165532 DOI: 10.1016/j.bios.2023.115178] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/20/2023] [Accepted: 02/22/2023] [Indexed: 03/05/2023]
Abstract
Seasonal outbreaks of respiratory viral infections remain a global concern, with increasing morbidity and mortality rates recorded annually. Timely and false responses contribute to the widespread of respiratory pathogenic diseases owing to similar symptoms at an early stage and subclinical infection. The prevention of emerging novel viruses and variants is also a big challenge. Reliable point-of-care diagnostic assays for early infection diagnosis play a critical role in the response to threats of epidemics or pandemics. We developed a facile method for specifically identifying different viruses based on surface-enhanced Raman spectroscopy (SERS) with pathogen-mediated composite materials on Au nanodimple electrodes and machine learning (ML) analyses. Virus particles were trapped in three-dimensional plasmonic concave spaces of the electrode via electrokinetic preconcentration, and Au films were simultaneously electrodeposited, leading to the acquisition of intense and in-situ SERS signals from the Au-virus composites for ultrasensitive SERS detection. The method was useful for rapid detection analysis (<15 min), and the ML analysis for specific identification of eight virus species, including human influenza A viruses (i.e., H1N1 and H3N2 strains), human rhinovirus, and human coronavirus, was conducted. The highly accurate classification was achieved using the principal component analysis-support vector machine (98.9%) and convolutional neural network (93.5%) models. This ML-associated SERS technique demonstrated high feasibility for direct multiplex detection of different virus species for on-site applications.
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Affiliation(s)
- Iris Baffour Ansah
- Nano-Bio Convergence Department, Korea Institute of Materials Science (KIMS), Changwon, Gyeongnam, 51508, Republic of Korea; Advanced Materials Engineering Division, University of Science and Technology (UST), Daejeon, 34113, Republic of Korea
| | - Matthew Leming
- Center for Systems Biology (CSB), Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Soo Hyun Lee
- Nano-Bio Convergence Department, Korea Institute of Materials Science (KIMS), Changwon, Gyeongnam, 51508, Republic of Korea
| | - Jun-Yeong Yang
- Nano-Bio Convergence Department, Korea Institute of Materials Science (KIMS), Changwon, Gyeongnam, 51508, Republic of Korea
| | - ChaeWon Mun
- Nano-Bio Convergence Department, Korea Institute of Materials Science (KIMS), Changwon, Gyeongnam, 51508, Republic of Korea
| | - Kyungseob Noh
- Infectious Diseases Therapeutic Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon, 34114, Republic of Korea; Graduate School of New Drug Discovery and Development, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Timothy An
- Infectious Diseases Therapeutic Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon, 34114, Republic of Korea; Graduate School of New Drug Discovery and Development, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Seunghun Lee
- Nano-Bio Convergence Department, Korea Institute of Materials Science (KIMS), Changwon, Gyeongnam, 51508, Republic of Korea
| | - Dong-Ho Kim
- Nano-Bio Convergence Department, Korea Institute of Materials Science (KIMS), Changwon, Gyeongnam, 51508, Republic of Korea; Advanced Materials Engineering Division, University of Science and Technology (UST), Daejeon, 34113, Republic of Korea
| | - Meehyein Kim
- Infectious Diseases Therapeutic Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon, 34114, Republic of Korea; Graduate School of New Drug Discovery and Development, Chungnam National University, Daejeon, 34134, Republic of Korea.
| | - Hyungsoon Im
- Center for Systems Biology (CSB), Massachusetts General Hospital, Boston, MA, 02114, USA; Department of Radiology, Massachusetts General Hospital, Boston, MA, 02114, USA.
| | - Sung-Gyu Park
- Nano-Bio Convergence Department, Korea Institute of Materials Science (KIMS), Changwon, Gyeongnam, 51508, Republic of Korea.
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Li H, Li Y, Gui C, Chen D, Chen L, Luo L, Huang G, Yuan Y, He R, Xia F, Wang J. Bare glassy nanopore for length-resolution reading of PCR amplicons from various pathogenic bacteria and viruses. Talanta 2023; 256:124275. [PMID: 36701856 DOI: 10.1016/j.talanta.2023.124275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 11/16/2022] [Accepted: 01/14/2023] [Indexed: 01/18/2023]
Abstract
In this study, it is confirmed that without addition of organic solvent and embedding polymer hydrogel into glass nanopore, bare glass nanopore can faithfully measure various lengths of DNA duplexes from 200 to 3000 base pairs with 200 base pairs resolution, showing well-separated peak amplitudes of blockage currents. Furthermore, motivated by this readout capability of duplex DNA, amplicons from Polymerase Chain Reaction (PCR) amplification are straightforwardly discriminated by bare glassy nanopore without fluorescent labeling. Except simultaneous discrimination of up to 7 different segments of the same lambda genome, various pathogenic bacteria and viruses including SARS-CoV-2 and its mutants in clinical samples can be discriminated at high resolution. Moreover, quantitative measurement of PCR amplicons is obtained with detection range spanning from 0.75 aM to 7.5 pM and detection limit of 7.5 aM, which reveals that bare glass nanopore can faithfully disclose PCR results without any extra labeling.
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Affiliation(s)
- Huizhen Li
- School of Chemistry and Chemical Engineering, School of Mechanical and Electrical Engineering, Guangzhou University, Guangzhou, Guangdong, 510006, China
| | - Yunhui Li
- School of Chemistry and Chemical Engineering, School of Mechanical and Electrical Engineering, Guangzhou University, Guangzhou, Guangdong, 510006, China
| | - Cenlin Gui
- School of Chemistry and Chemical Engineering, School of Mechanical and Electrical Engineering, Guangzhou University, Guangzhou, Guangdong, 510006, China
| | - Daqi Chen
- School of Chemistry and Chemical Engineering, School of Mechanical and Electrical Engineering, Guangzhou University, Guangzhou, Guangdong, 510006, China
| | - Lanfang Chen
- School of Chemistry and Chemical Engineering, School of Mechanical and Electrical Engineering, Guangzhou University, Guangzhou, Guangdong, 510006, China
| | - Le Luo
- School of Chemistry and Chemical Engineering, School of Mechanical and Electrical Engineering, Guangzhou University, Guangzhou, Guangdong, 510006, China
| | - Guobao Huang
- Guangxi Key Laboratory of Agricultural Resources Chemistry and Biotechnology, College of Chemistry and Food Science, Yulin Normal University, Yulin, Guangxi, 537000, China
| | - Yang Yuan
- School of Chemistry and Chemical Engineering, School of Mechanical and Electrical Engineering, Guangzhou University, Guangzhou, Guangdong, 510006, China
| | - Rong He
- Guangzhou Center for Disease Control and Prevention, Guangzhou, Guangdong, 510440, China.
| | - Fan Xia
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, Hubei, 430074, China.
| | - Jiahai Wang
- School of Chemistry and Chemical Engineering, School of Mechanical and Electrical Engineering, Guangzhou University, Guangzhou, Guangdong, 510006, China.
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CRISPR-Cas12a-assisted elimination of the non-specific signal from non-specific amplification in the Exponential Amplification Reaction. Anal Chim Acta 2023; 1251:340998. [PMID: 36925288 DOI: 10.1016/j.aca.2023.340998] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/13/2023] [Accepted: 02/21/2023] [Indexed: 02/24/2023]
Abstract
Non-specific amplification is a major problem in nucleic acid amplification resulting in false-positive results, especially for exponential amplification reactions (EXPAR). Although efforts were made to suppress the influence of non-specific amplification, such as chemical blocking of the template's 3'-ends and sequence-independent weakening of template-template interactions, it is still a common problem in many conventional EXPAR reactions. In this study, we propose a novel strategy to eliminate the non-specific signal from non-specific amplification by integrating the CRISPR-Cas12a system into two-templates EXPAR. An EXPAR-Cas12a strategy named EXPCas was developed, where the Cas12a system acted as a filter to filter out non-specific amplificons in EXPAR, suppressing and eliminating the influence of non-specific amplification. As a result, the signal-to-background ratio was improved from 1.3 to 15.4 using this method. With microRNA-21 (miRNA-21) as a target, the detection can be finished in 40 min with a LOD of 103 fM and no non-specific amplification was observed.
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40
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Fang L, Yang L, Han M, Xu H, Ding W, Dong X. CRISPR-cas technology: A key approach for SARS-CoV-2 detection. Front Bioeng Biotechnol 2023; 11:1158672. [PMID: 37214290 PMCID: PMC10198440 DOI: 10.3389/fbioe.2023.1158672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 03/31/2023] [Indexed: 05/24/2023] Open
Abstract
The CRISPR (Clustered Regularly Spaced Short Palindromic Repeats) system was first discovered in prokaryotes as a unique immune mechanism to clear foreign nucleic acids. It has been rapidly and extensively used in basic and applied research owing to its strong ability of gene editing, regulation and detection in eukaryotes. Hererin in this article, we reviewed the biology, mechanisms and relevance of CRISPR-Cas technology and its applications in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnosis. CRISPR-Cas nucleic acid detection tools include CRISPR-Cas9, CRISPR-Cas12, CRISPR-Cas13, CRISPR-Cas14, CRISPR nucleic acid amplification detection technology, and CRISPR colorimetric readout detection system. The above CRISPR technologies have been applied to the nucleic acid detection, including SARS-CoV-2 detection. Common nucleic acid detection based on CRISPR derivation technology include SHERLOCK, DETECTR, and STOPCovid. CRISPR-Cas biosensing technology has been widely applied to point-of-care testing (POCT) by targeting recognition of both DNA molecules and RNA Molecules.
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Affiliation(s)
- Lijuan Fang
- Department of Laboratory Medicine, Hangzhou Ninth People’s Hospital, Hangzhou, Zhejiang Province, China
| | - Lusen Yang
- Department of Laboratory Medicine, Hangzhou Ninth People’s Hospital, Hangzhou, Zhejiang Province, China
| | - Mingyue Han
- Department of Laboratory Medicine, Hangzhou Ninth People’s Hospital, Hangzhou, Zhejiang Province, China
| | - Huimei Xu
- Department of Laboratory Medicine, Hangzhou Ninth People’s Hospital, Hangzhou, Zhejiang Province, China
| | - Wenshuai Ding
- Department of Laboratory Medicine, Hangzhou Ninth People’s Hospital, Hangzhou, Zhejiang Province, China
| | - Xuejun Dong
- Medical Laboratory, Zhejiang University Shaoxing Hospital, Shaoxing, China
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41
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Liu FX, Cui JQ, Wu Z, Yao S. Recent progress in nucleic acid detection with CRISPR. LAB ON A CHIP 2023; 23:1467-1492. [PMID: 36723235 DOI: 10.1039/d2lc00928e] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Recent advances in CRISPR-based biotechnologies have greatly expanded our capabilities to repurpose CRISPR for the development of molecular diagnostic systems. The key attribute that allows CRISPR to be widely utilized is its programmable and highly specific nature. In this review, we first illustrate the principle of the class 2 CRISPR nucleases for molecular diagnostics which originates from their immunologic defence systems. Next, we present the CRISPR-based schemes in the application of diagnostics with amplification-assisted or amplification-free strategies. By highlighting some of the recent advances we interpret how general bioengineering methodologies can be integrated with CRISPR. Finally, we discuss the challenges and exciting prospects for future CRISPR-based biosensing development. We hope that this review will guide the reader to systematically learn the start-of-the-art development of CRISPR-mediated nucleic acid detection and understand how to apply the CRISPR nucleases with different design concepts to more general applications in diagnostics and beyond.
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Affiliation(s)
- Frank X Liu
- Department of Mechanical and Aerospace Engineering, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
| | - Johnson Q Cui
- Department of Mechanical and Aerospace Engineering, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
| | - Zhihao Wu
- IIP-Advanced Materials, Interdisciplinary Program Office (IPO), Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Shuhuai Yao
- Department of Mechanical and Aerospace Engineering, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
- Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
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42
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Jiang Y, Zheng C, Jin M, Zhou R, Wu Q, Huang F, Lou Y, Zheng L. An Ultrasensitive Colorimetric Foodborne Pathogenic Detection Method Using a CRISPR/Cas12a Mediated Strand Displacement/Hybridization Chain Reaction. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:4193-4200. [PMID: 36812357 DOI: 10.1021/acs.jafc.2c08888] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Accurate, rapid, and sensitive pathogenic detections play an important role in food safety. Herein, we developed a novel CRISPR/Cas12a mediated strand displacement/hybridization chain reaction (CSDHCR) nucleic acid assay for foodborne pathogenic colorimetric detection. A biotinylated DNA toehold is coupled on avidin magnetic beads and acts as an initiator strand to trigger the SDHCR. The SDHCR amplification allowed the formation of long hemin/G-quadruplex-based DNAzyme products to catalyze the TMB-H2O2 reaction. In the presence of the DNA targets, the trans-cleavage activity of CRISPR/Cas12a was activated to cleave the initiator DNA, resulting in the failure of SDHCR and no color change. Under optimal conditions, the CSDHCR has a satisfactory linear detection of DNA targets with a regression equation Y = 0.0531*X - 0.0091 (R2 = 0.9903) in the range of 10 fM to 1 nM, and the limit of detection was determined as 4.54 fM. In addition, Vibrio vulnificus, one foodborne pathogen, was used to verify the practical application of the method, and it showed satisfactory specificity and sensitivity with a limit of detection at 1.0 × 100 CFU/mL coupling with recombinase polymerase amplification. Our proposed CSDHCR biosensor could be a promising alternative method for ultrasensitive and visual detection of nucleic acids and the practical application of foodborne pathogens.
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Affiliation(s)
- Yayun Jiang
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China 325035
- Department of Clinical Laboratory, People's Hospital of Deyang City, Deyang, China 618000
| | - Chaochuan Zheng
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China 325035
| | - Ming Jin
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China 325035
| | - Ruolan Zhou
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China 325035
| | - Qiaoli Wu
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China 325035
| | - Fuyuan Huang
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China 325035
| | - Yongliang Lou
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China 325035
| | - Laibao Zheng
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China 325035
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43
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Li Z, Uno N, Ding X, Avery L, Banach D, Liu C. Bioinspired CRISPR-Mediated Cascade Reaction Biosensor for Molecular Detection of HIV Using a Glucose Meter. ACS NANO 2023; 17:3966-3975. [PMID: 36762838 PMCID: PMC10198471 DOI: 10.1021/acsnano.2c12754] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
HIV molecular detection plays a significant role in early diagnosis and antiretroviral therapy for HIV patients. CRISPR technology has recently emerged as a powerful tool for highly sensitive and specific nucleic acid based molecular detection when used in combination with isothermal amplification. However, it remains a challenge to improve the compatibility of such a multienzyme reaction system for simple and sensitive molecular detection. Inspired by the multicompartment structures in a living cell, we present a nanoporous membrane-separated (compartmentalized), artificial, cascade reaction system to improve the compatibility of a CRISPR-mediated multienzyme reaction. We further integrated the multienzyme cascade reaction system with a microfluidic platform and glucose biosensing technology to develop a bioinspired, CRISPR-mediated cascade reaction (CRISPR-MCR) biosensor, enabling HIV molecular detection by a simple glucose meter, analogous to diabetes home testing. We applied the bioinspired CRISPR-MCR biosensor to detect HIV DNA and HIV RNA, achieving a detection sensitivity of 43 copies and 200 copies per test, respectively. Further, we successfully validated the bioinspired biosensor by testing clinical plasma samples of HIV, demonstrating its great application potential for point-of-care testing of HIV virus and other pathogens at home or in resource-limited settings.
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Affiliation(s)
- Ziyue Li
- Department of Biomedical Engineering, University of Connecticut Health Center, Farmington, CT 06030, United States
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT 06269, United States
| | - Naoki Uno
- Department of Biomedical Engineering, University of Connecticut Health Center, Farmington, CT 06030, United States
| | - Xiong Ding
- Department of Biomedical Engineering, University of Connecticut Health Center, Farmington, CT 06030, United States
| | - Lori Avery
- Department of Pathology and Laboratory Medicine, University of Connecticut Health Center, Farmington, CT 06030, United States
| | - David Banach
- Department of Medicine, Division of Infectious Diseases, University of Connecticut Health Center, Farmington, CT 06030, United States
| | - Changchun Liu
- Department of Biomedical Engineering, University of Connecticut Health Center, Farmington, CT 06030, United States
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44
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Xu S, Wang S, Guo L, Tong Y, Wu L, Huang X. Nanozyme-catalysed CRISPR-Cas12a system for the preamplification-free colorimetric detection of lead ion. Anal Chim Acta 2023; 1243:340827. [PMID: 36697180 DOI: 10.1016/j.aca.2023.340827] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/21/2022] [Accepted: 01/11/2023] [Indexed: 01/14/2023]
Abstract
CRISPR-based detection was often based on the target preamplification to realize the high sensitivity. Here, we prepared a CRISPR-Cas12a system for the colorimetric detection of lead ion (Pb2+) based on the assistance of DNAzyme and nanozyme instead of preamplification. The recognition between GR-5 DNAzyme and Pb2+ could trigger the CRISPR-Cas12a system. MnO2 nanozymes connected with magnetic beads through single stranded DNA were prepared as the colorimetric signal probes and catalyst of CRISPR-Cas12a system for the strong oxidase-like activity inducing the color change of 3,3',5,5'-tetramethylbenzidine. The nanozyme-catalysed CRISPR-Cas12a system could be used to detect Pb2+ through the color change with high specificity and sensitivity. The linear range of this approach was 0.8 nM-2500 nM, with a limit of detection of 0.54 nM. This method was applied for the detection of the Pb2+ in food samples indicating good accuracy and anti-interference ability.
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Affiliation(s)
- Shiqi Xu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Songtao Wang
- National Engineering Research Center of Solid-state Brewing, Luzhou, 646000, China
| | - Ling Guo
- Zhejiang Laboratory, Hangzhou, 311100, China
| | - Yuqin Tong
- National Engineering Research Center of Solid-state Brewing, Luzhou, 646000, China
| | - Lina Wu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China.
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45
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Shao F, Park JS, Zhao G, Hsieh K, Wang TH. Elucidating the Role of CRISPR/Cas in Single-Step Isothermal Nucleic Acid Amplification Testing Assays. Anal Chem 2023; 95:3873-3882. [PMID: 36745596 PMCID: PMC10884613 DOI: 10.1021/acs.analchem.2c05632] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Developing assays that combine CRISPR/Cas and isothermal nucleic acid amplification has become a burgeoning research area due to the novelty and simplicity of CRISPR/Cas and the potential for point-of-care uses. Most current research explores various two-step assays by appending different CRISPR/Cas effectors to the end of different isothermal nucleic acid amplification methods. However, efforts in integrating both components into more ideal single-step assays are scarce, and poor-performing single-step assays have been reported. Moreover, lack of investigations into CRISPR/Cas in single-step assays results in incomplete understanding. To fill this knowledge gap, we conducted a systematic investigation by developing and comparing assays that share the identical recombinase polymerase amplification (RPA) but differ in CRISPR/Cas12a. We found that the addition of CRISPR/Cas12a indeed unlocks signal amplification but, at the same time, impedes RPA and that CRISPR/Cas12a concentration is a key parameter for attenuating RPA impediment and ensuring assay performance. Accordingly, we found that our protospacer adjacent motif (PAM)-free CRISPR/Cas12a-assisted RPA assay, which only moderately impeded RPA at its optimal CRISPR/Cas12a concentration, outperformed its counterparts in assay design, signal, sensitivity, and speed. We also discovered that a new commercial Cas12a effector could also drive our PAM-free CRISPR/Cas12a-assisted RPA assay and reduce its cost, though simultaneously lowering its signal. Our study and the new insights can be broadly applied to steer and facilitate further advances in CRISPR/Cas-based assays.
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Affiliation(s)
- Fangchi Shao
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Joon Soo Park
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Guojie Zhao
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Kuangwen Hsieh
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Tza-Huei Wang
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
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46
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Wang H, Xu J, Li S, Wang X, Liu G, Yang S, Zhao F, Liu Q, Chen X, He C, Li M. An integrated dual-layer microfluidic platform for multiple respiratory viruses screening. Anal Chim Acta 2023; 1242:340812. [PMID: 36657884 PMCID: PMC9822946 DOI: 10.1016/j.aca.2023.340812] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 12/31/2022] [Accepted: 01/06/2023] [Indexed: 01/09/2023]
Abstract
Currently, the coronavirus disease 2019 (COVID-19) caused by the outbreak of a novel coronavirus (SARS-CoV-2) is spreading rapidly worldwide. Due to the high incidence of influenza coinciding with SARS-CoV-2, rapid detection is crucial to prevent spreading. Here, we present an integrated dual-layer microfluidic platform for specific and highly sensitive SARS-CoV-2, influenza viruses A (FluA) H1N1, H3N2, and influenza virus B (FluB) simultaneous detection. The platform includes a dual microchip (Dμchip) and a portable detection device for real-time fluorescence detection, temperature control and online communication. The Reverse Transcription Loop-mediated Isothermal Amplification (RT-LAMP) and Cas12a cleavage were performed on the Dμchip. The limit of detection (LoD) of the Dμchip assay was 10 copies for SARS-CoV-2, FluA H1N1, H3N2, and FluB RNAs. The Dμchip assay yielded no cross-reactivity against other coronaviruses, so it was suitable for the screening of multiple viruses. Moreover, the positive percentage agreement (PPA) and negative percentage agreement (NPA) of the assay were 97.9% and 100%, respectively, in 75 clinical samples compared to data from RT-PCR-based assays. Furthermore, the assay allowed the detection SARS-CoV-2 and influenza viruses in spiked samples. Overall, the present platform would provide a rapid method for the screening of multiple viruses in hospital emergency, community and primary care settings and facilitate the remote diagnosis and outbreak control of the COVID-19.
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Affiliation(s)
- Hua Wang
- Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China,Corresponding author
| | - Jingsong Xu
- Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Shun Li
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Xi Wang
- Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Gang Liu
- Bio Metrology Laboratory, Chemical and Ionizing Radiation Metrolology Institute, Shanghai Institute of Measurement and Testing Technology, Shanghai, China
| | - Shuang Yang
- Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Fei Zhao
- National Key Laboratory of Science and Technology on Micro/Nano Fabrication, Department of Micro/Nano Electronics, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qian Liu
- Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Xiang Chen
- National Key Laboratory of Science and Technology on Micro/Nano Fabrication, Department of Micro/Nano Electronics, Shanghai Jiao Tong University, Shanghai 200240, China,Corresponding author
| | - Chao He
- Department of Laboratory Medicine, West China Hospital of Sichuan University, Sichuan, China,Corresponding author
| | - Min Li
- Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China,Corresponding author
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47
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Liu S, Xie T, Pei X, Li S, He Y, Tong Y, Liu G. CRISPR-Cas12a coupled with universal gold nanoparticle strand-displacement probe for rapid and sensitive visual SARS-CoV-2 detection. SENSORS AND ACTUATORS. B, CHEMICAL 2023; 377:133009. [PMID: 36439054 PMCID: PMC9678389 DOI: 10.1016/j.snb.2022.133009] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/04/2022] [Accepted: 11/16/2022] [Indexed: 05/27/2023]
Abstract
Point of care (POC) diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are particularly significant for preventing transmission of coronavirus disease 2019 (COVID-19) by any user at any given time and place. CRISPR/Cas-assisted SARS-CoV-2 assays are viewed as supplemental to RT-PCR due to simple operation, convenient use and low cost. However, most current CRISPR molecular diagnostics based on fluorescence measurement increased the difficulty of POC test with need of the additional light sources. Some instrument-free visual detection with the naked eye has limitations in probe universality. Herein, we developed a universal, rapid, sensitive and specific SARS-CoV-2 POC test that combines the outstanding DNase activity of Cas12a with universal AuNPs strand-displacement probe. The oligo trigger, which is the switch the AuNPs of the strand-displacement probe, is declined as a result of Cas12a recognition and digestion. The amount of released AuNPs produced color change which can be visual with the naked eye and assessed by UV-Vis spectrometer for quantitative detection. Furthermore, a low-cost hand warmer is used as an incubator for the visual assay, enabling an instrument-free, visual SARS-CoV-2 detection within 20 min. A real coronavirus GX/P2V instead of SARS-CoV-2 were chosen for practical application validation. After rapid virus RNA extraction and RT-PCR amplification, a minimum of 2.7 × 102 copies/mL was obtained successfully. The modular design can be applied to many nucleic acid detection applications, such as viruses, bacteria, species, etc., by simply modifying the crRNA, showing great potential in POC diagnosis.
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Affiliation(s)
- Sitong Liu
- College of Chemistry and Materials Engineering and Institute of Cosmetic Regulatory Science, Beijing Technology and Business University, Beijing 100048, PR China
| | - Tie Xie
- College of Chemistry and Materials Engineering, Beijing Technology and Business University, Beijing 100048, PR China
| | - Xiaojing Pei
- College of Chemistry and Materials Engineering and Institute of Cosmetic Regulatory Science, Beijing Technology and Business University, Beijing 100048, PR China
| | - Shujing Li
- College of Chemistry and Materials Engineering and Institute of Cosmetic Regulatory Science, Beijing Technology and Business University, Beijing 100048, PR China
| | - Yifan He
- College of Chemistry and Materials Engineering and Institute of Cosmetic Regulatory Science, Beijing Technology and Business University, Beijing 100048, PR China
| | - Yigang Tong
- College of Chemistry and Materials Engineering, Beijing Technology and Business University, Beijing 100048, PR China
| | - Guoqi Liu
- Biotecnovo (Beijing) Co.,LTD, Beijing Economic and Technological Development Zone, Beijing, PR China
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48
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He H, Zhou Y, Chen B, Zhang Y, Zhong X, Xu L, Guo B, Yin C, Zhou X, Li Q, Huang Z, Luo G, Guo X. Nucleic acid amplification with specific signal filtration and magnification for ultrasensitive colorimetric detection. Talanta 2023; 253:123978. [PMID: 36209643 DOI: 10.1016/j.talanta.2022.123978] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/20/2022] [Accepted: 09/27/2022] [Indexed: 11/23/2022]
Abstract
Recently, sensitive, fast and low cost nucleic acid isothermal amplification technologies (such as loop-mediated isothermal amplification, LAMP) have attracted great attention in the urgent needs of point-of-care testing (POCT) and regular epidemic prevention and control. However, unlike PCR which usually employs TaqMan probe to report specific signals, specific-signal-output strategies in isothermal amplification are immature and visual detection even rare, which limits their popularity in POCT. We hypothesize to address this issue by designing a visual-signal-report system to both filtrate and magnify the target information in isothermal amplification. In this work, we developed a specific signal filtration and magnification colorimetric isothermal sensing platform (SFMC for short) for ultrasensitive detection of DNA and RNA. SFMC consists of two processes: an isothermal amplification with specific signal filtration and a self-replication catalyzed hairpin assembly (SRCHA) for rapid target-specific signal magnification and outputting. With these unique properties, this biosensing platform could detect target DNA as low as 5 copies per reaction and target RNA as low as 10 copies per reaction by naked eyes. Benefited from the excellent colorimetric detection performance, this biosensing platform has been successfully used for African swine fever virus (ASFV) and SARS-CoV-2 detection.
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Affiliation(s)
- Hongfei He
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Translational Medicine Research Center & Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, 637000, PR China
| | - Yan Zhou
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Translational Medicine Research Center & Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, 637000, PR China; School of Pharmacy & School of Preclinical Medicine, North Sichuan Medical College, Nanchong, 637000, PR China
| | - Bin Chen
- Sichuan Provincial Center for Animal Disease Control and Prevention, Chengdu, 610041, PR China
| | - Yi Zhang
- Sichuan Provincial Center for Animal Disease Control and Prevention, Chengdu, 610041, PR China
| | - Xiaowu Zhong
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Translational Medicine Research Center & Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, 637000, PR China
| | - Lei Xu
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Translational Medicine Research Center & Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, 637000, PR China
| | - Bin Guo
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Translational Medicine Research Center & Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, 637000, PR China
| | - Chong Yin
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Translational Medicine Research Center & Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, 637000, PR China
| | - Xi Zhou
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Translational Medicine Research Center & Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, 637000, PR China
| | - Qingrong Li
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Translational Medicine Research Center & Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, 637000, PR China
| | - Zhen Huang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, PR China.
| | - Guangcheng Luo
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Translational Medicine Research Center & Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, 637000, PR China.
| | - Xiaolan Guo
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Translational Medicine Research Center & Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, 637000, PR China.
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49
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Liu J, Ge C, Zha L, Lin L, Li R. Simple Nano-Luciferase-Based Assay for the Rapid and High-Throughput Detection of SARS-CoV-2 3C-Like Protease. Anal Chem 2023; 95:714-719. [PMID: 36576396 PMCID: PMC9843625 DOI: 10.1021/acs.analchem.2c02590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 12/09/2022] [Indexed: 12/29/2022]
Abstract
In this study, we described an easy-to-perform nano-luciferase (nLuc) sensor for the rapid detection of 3-chymotrypsin-like protease (3CLpro) encoded by SARS-CoV-2. The technology is based on the cleavage reaction of recombinant-nLuc via 3CLpro. The nLuc-based assay is a general, one-step method and is naturally specific in detection. The stability, sensitivity, detection range, and response time are fully characterized. The application of 3CLpro detection in artificial and human saliva as well as antiviral drug screening demonstrates that the method can quantify 3CLpro with high sensitivity in one step. With its unique features, the nLuc-based assay may find broad applications in the auxiliary diagnosis of SARS-CoV-2, as well as other types of coronavirus infection.
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Affiliation(s)
- Jingxin Liu
- College
of Health Science and Environmental Engineering, Shenzhen Technology University, 3002 Lantian Road, Pingshan District, Shenzhen, Guangdong 518118, P. R. China
| | - Chenchen Ge
- College
of Health Science and Environmental Engineering, Shenzhen Technology University, 3002 Lantian Road, Pingshan District, Shenzhen, Guangdong 518118, P. R. China
| | - Ling Zha
- College
of Health Science and Environmental Engineering, Shenzhen Technology University, 3002 Lantian Road, Pingshan District, Shenzhen, Guangdong 518118, P. R. China
| | - Ligen Lin
- State
Key Laboratory of Quality Research in Chinese Medicine, Institute
of Chinese Medical Sciences, University
of Macau, Macao 999078, P. R. China
| | - Rongsong Li
- College
of Health Science and Environmental Engineering, Shenzhen Technology University, 3002 Lantian Road, Pingshan District, Shenzhen, Guangdong 518118, P. R. China
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50
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Yang Y, Yi W, Gong F, Tan Z, Yang Y, Shan X, Xie C, Ji X, Zheng Z, He Z. CRISPR/Cas13a Trans-Cleavage-Triggered Catalytic Hairpin Assembly Assay for Specific and Ultrasensitive SARS-CoV-2 RNA Detection. Anal Chem 2023; 95:1343-1349. [PMID: 36571299 PMCID: PMC9843626 DOI: 10.1021/acs.analchem.2c04306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 12/16/2022] [Indexed: 12/27/2022]
Abstract
New coronavirus (SARS-CoV-2), which has caused the coronavirus disease 2019 (COVID-19) pandemic, has brought about a huge burden on global healthcare systems. Rapid and early detection is important to prevent the spread of the pandemic. Here, an assay based on CRISPR/Cas13a and catalytic hairpin assembly (CHA), termed as Cas-CHA, was developed for ultrasensitive and specific detection of SARS-CoV-2 RNA. Upon specific recognition of the target, the CRISPR/Cas13a collaterally cleaved a well-designed hairpin reporter and triggered the CHA reaction. Under optimized conditions, the assay detected the SARS-CoV-2 RNA with a wide range of 100 aM to 100 nM and realized a low detection limit of 84 aM. At the same time, the whole detecting process could be completed within 35 min. More importantly, the assay was able to distinguish SARS-CoV-2 RNA from common human coronaviruses and analyze in saliva samples. By the flexible design of crRNA, the assay was expanded to detect other viruses. The clinical sample analysis verified that the proposed assay held a great potential for practical testing.
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Affiliation(s)
- Yixia Yang
- College
of Chemistry and Molecular Sciences, Wuhan
University, Wuhan 430072, China
| | - Wenfu Yi
- State
Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Feng Gong
- College
of Chemistry and Molecular Sciences, Wuhan
University, Wuhan 430072, China
| | - Zhiyou Tan
- College
of Chemistry and Molecular Sciences, Wuhan
University, Wuhan 430072, China
| | - Yeling Yang
- College
of Chemistry and Molecular Sciences, Wuhan
University, Wuhan 430072, China
| | - Xiaoyun Shan
- College
of Chemistry and Molecular Sciences, Wuhan
University, Wuhan 430072, China
| | - Conghua Xie
- Department
of Radiation and Medical Oncology, Hubei Key Laboratory of Tumor Biological
Behaviors, and Hubei Cancer Clinical Study Center, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Xinghu Ji
- College
of Chemistry and Molecular Sciences, Wuhan
University, Wuhan 430072, China
| | - Zhenhua Zheng
- State
Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Zhike He
- College
of Chemistry and Molecular Sciences, Wuhan
University, Wuhan 430072, China
- Wuhan
Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan 430071, China
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